Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dy...

Full description

Saved in:
Bibliographic Details
Published inPhysics of life reviews Vol. 10; no. 1; pp. 1 - 26
Main Author Micheletti, Cristian
Format Journal Article
LanguageEnglish
Published Netherlands Elsevier B.V 01.03.2013
Subjects
Animals
Databases, Protein
Humans
Molecular Dynamics Simulation
PDZ Domains
Peptide Hydrolases - chemistry
Peptide Hydrolases - metabolism
Proteins - chemistry
Proteins - metabolism
Structural Homology, Protein
Structure-Activity Relationship
Online AccessGet full text

Cover

Abstract The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure–function relationship.
AbstractList The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional structural elements, those aspects of protein flexibility and dynamics that are functionally oriented should be subject to evolutionary conservation. Accordingly, dynamics-based protein comparisons or alignments could be used to detect protein relationships that are more elusive to sequence and structural alignments. Here we provide an account of the progress that has been made in recent years towards developing and applying general methods for comparing proteins in terms of their internal dynamics and advance the understanding of the structure-function relationship.
Author Micheletti, Cristian
Author_xml – sequence: 1
  givenname: Cristian
  surname: Micheletti
  fullname: Micheletti, Cristian
  email: michelet@sissa.it
  organization: Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, Trieste, Italy
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23199577$$D View this record in MEDLINE/PubMed
BookMark eNqFkU1uFDEQhS0URH7gBEiol9n0YLvdPxWJBRolJFIkNrC2PO7qxCO33bHdEbMid8gNcxI8MyELFmTlUul7T673jsmB8w4J-cjoglHWfF4vJhvwfsEp43mzoBTekCPWtVXJRN0e5LluWUkbUR-S4xjXlFZcdPQdOeQVA6jb9oj8XvpxUsG4m2IKPqFxsVhtinSLJhTGJQxO2aLfODUaHc-K81-T9Ts8pjDrNAd8engcZqeT8a4IaNV2iLdmyka48a7PZN7pF0H2U9bcuBFdiu_J20HZiB-e3xPy8-L8x_KyvP7-7Wr59brUVQ2pHAY9iKrTKDgo6MQKcGgQBOSjmVKCdZxTAUNHoW2BNUxDB82q47QBYJpWJ-R075uvvJsxJjmaqNFa5dDPUbKKZwugbZPRT8_ovBqxl1Mwowob-Te0DFR7QAcfY8DhBWFUbquRa7mrRm6r2S7zL7MK_lFpk3ZhpaCMfUX7Za_FHNG9wSCjNug09iagTrL35r_6P79Brvw
CitedBy_id crossref_primary_10_1371_journal_pone_0138118
crossref_primary_10_1039_C3CS60474H
crossref_primary_10_1098_rsif_2014_0419
crossref_primary_10_1021_acs_jpcb_0c05347
crossref_primary_10_1371_journal_pone_0183889
crossref_primary_10_1063_1_4885338
crossref_primary_10_1093_cvr_cvy040
crossref_primary_10_1002_bies_201300134
crossref_primary_10_1080_07391102_2021_2021990
crossref_primary_10_1371_journal_pone_0128954
crossref_primary_10_1002_prot_25454
crossref_primary_10_1186_1471_2148_14_78
crossref_primary_10_1093_bib_bbz146
crossref_primary_10_1371_journal_pone_0226147
crossref_primary_10_1002_wcms_1186
crossref_primary_10_1016_j_jinorgbio_2023_112343
crossref_primary_10_1073_pnas_1712021114
crossref_primary_10_1093_nar_gkv708
crossref_primary_10_3389_fgene_2018_00182
crossref_primary_10_1007_s10858_024_00449_4
crossref_primary_10_1016_j_str_2015_05_022
crossref_primary_10_1002_prot_24565
crossref_primary_10_1016_j_jmgm_2016_12_003
crossref_primary_10_1016_j_str_2015_10_025
crossref_primary_10_1016_j_sbi_2017_12_001
crossref_primary_10_1093_molbev_msu281
crossref_primary_10_1093_bioinformatics_btab062
crossref_primary_10_1016_j_sbi_2020_08_009
crossref_primary_10_1021_acs_analchem_1c02155
crossref_primary_10_1098_rsif_2019_0075
crossref_primary_10_1021_acs_jctc_7b00997
crossref_primary_10_7717_peerj_11330
crossref_primary_10_1039_D2SC01078J
crossref_primary_10_1186_s12859_014_0427_6
crossref_primary_10_1039_C6CP03666J
crossref_primary_10_33380_2305_2066_2025_14_1_1889
crossref_primary_10_1107_S2059798322001966
crossref_primary_10_1016_j_plrev_2012_10_005
crossref_primary_10_1021_acs_biochem_8b01004
crossref_primary_10_1371_journal_pcbi_1004834
crossref_primary_10_1016_j_plrev_2012_10_010
crossref_primary_10_1002_prot_25311
crossref_primary_10_1093_molbev_msz102
crossref_primary_10_1016_j_str_2014_03_006
crossref_primary_10_1080_07391102_2020_1753577
crossref_primary_10_1002_ijch_201300142
crossref_primary_10_1021_acs_jcim_9b00006
crossref_primary_10_1073_pnas_2110553118
crossref_primary_10_1371_journal_pcbi_1004826
crossref_primary_10_1007_s00894_020_04557_4
crossref_primary_10_1002_prot_25598
crossref_primary_10_1016_j_bpj_2021_11_2888
crossref_primary_10_1093_bioinformatics_btt324
crossref_primary_10_1093_bioinformatics_btu336
crossref_primary_10_1080_23312025_2017_1291877
crossref_primary_10_1515_jbcpp_2020_0369
crossref_primary_10_1371_journal_pone_0208465
crossref_primary_10_1002_jcc_24803
crossref_primary_10_3390_ijms22147625
crossref_primary_10_1016_j_csbj_2020_02_017
crossref_primary_10_1016_j_jsb_2018_05_006
Cites_doi 10.2174/138920309787847608
10.1002/bip.360230610
10.1371/journal.pcbi.1000331
10.1016/0022-2836(85)90230-X
10.1002/prot.10628
10.1016/S0022-2836(05)80134-2
10.1038/357543a0
10.1002/prot.24017
10.1101/gr.3133605
10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
10.1371/journal.pcbi.0030121
10.1093/nar/gkh034
10.1073/pnas.2135471100
10.1021/bi052101l
10.2174/138920309787847590
10.1103/PhysRevLett.98.048102
10.1002/prot.21652
10.1103/PhysRevLett.94.198302
10.1007/s00018-009-0014-6
10.1038/nsmb.2208
10.1002/prot.22855
10.1021/ml900003t
10.1371/journal.pcbi.1002154
10.1016/j.bpj.2009.03.051
10.1073/pnas.0711732105
10.1016/S0022-2836(03)00734-4
10.1002/(SICI)1097-0134(199703)27:3<425::AID-PROT10>3.0.CO;2-N
10.1126/science.273.5275.595
10.1371/journal.pcbi.1002749
10.1110/ps.073390208
10.1103/PhysRevLett.84.3009
10.1103/PhysRevLett.95.198103
10.1038/35018538
10.1002/prot.20672
10.1007/s00239-005-0209-x
10.1093/nar/gkn570
10.1016/S1359-0278(97)00024-2
10.1016/S0022-2836(02)00562-4
10.1038/nsmb.1682
10.1021/bi00188a001
10.1093/nar/gki087
10.1371/journal.pcbi.1002193
10.1016/j.gene.2008.06.002
10.1093/nar/gki024
10.1103/PhysRevLett.87.088102
10.1002/pro.5560071126
10.1146/annurev.bb.17.060188.002315
10.1021/ct050051s
10.1529/biophysj.106.083568
10.1351/PAC-CON-12-02-15
10.1093/nar/gkh430
10.1088/0953-8984/19/28/285206
10.1002/prot.22139
10.1073/pnas.0704422105
10.1103/PhysRevLett.82.3372
10.1002/prot.20836
10.1126/science.286.5438.295
10.1093/molbev/msp020
10.1021/pr070314m
10.1038/nature06410
10.1021/cr040669e
10.1016/S0006-3495(01)76033-X
10.1021/ja809915a
10.1002/prot.20268
10.1016/j.str.2005.01.017
10.1016/0263-7855(96)00018-5
10.1126/science.275.5296.73
10.1002/prot.10168
10.1186/1471-2105-11-188
10.1073/pnas.80.12.3696
10.1021/bi0518085
10.1002/prot.340170408
10.1103/PhysRevLett.104.228103
10.1016/S0022-2836(02)00301-7
10.1016/S0006-3495(00)76756-7
10.1073/pnas.052005999
10.1093/bioinformatics/btr497
10.1146/annurev.biochem.74.082803.133029
10.1103/PhysRevLett.68.2696
10.1146/annurev.biochem.75.110105.142336
10.1002/jcc.540161209
10.1186/1472-6807-9-6
10.1073/pnas.93.25.14243
10.1021/ct100208e
10.1016/j.bpc.2005.07.004
10.1110/ps.0206702
10.1002/prot.21353
10.1146/annurev.physchem.58.032806.104449
10.1038/262325a0
10.1016/0022-2836(70)90057-4
10.1093/molbev/mss097
10.1110/ps.0215902
10.1103/PhysRevLett.77.1905
10.1073/pnas.0907548106
10.1529/biophysj.104.053041
10.1021/bi801102e
10.1371/journal.pone.0033931
10.1021/ja0026814
10.1126/science.1086911
10.1110/ps.03468904
10.1093/nar/gkq293
10.1016/j.jmb.2005.01.058
10.1529/biophysj.107.105270
10.1126/science.1069823
10.1007/s00239-005-0289-7
10.1016/S0006-3495(00)76527-1
10.1016/B978-0-12-386485-7.00005-3
10.1021/jp0751716
10.1093/nar/gkh027
10.1093/protein/14.1.1
10.1093/bioinformatics/16.6.566
10.1073/pnas.0907683106
10.1098/rstb.2005.1802
10.1038/nature06407
10.1126/science.1123539
10.1529/biophysj.104.052449
10.1146/annurev.biochem.77.062706.154450
10.1371/journal.pone.0015827
10.1016/j.str.2007.03.013
10.1002/prot.22553
10.1016/j.str.2011.03.009
10.1371/journal.pcbi.1002433
10.1126/science.1198542
10.1093/nar/25.24.4876
10.1529/biophysj.104.055004
10.1126/science.1749933
10.1146/annurev.biochem.75.103004.142800
10.1172/JCI6509
10.1002/(SICI)1097-0134(19990215)34:3<369::AID-PROT9>3.0.CO;2-F
10.1021/ja044608+
10.1103/PhysRevE.65.031910
10.1021/ja100002b
10.1093/bioinformatics/btp506
10.1093/bioinformatics/bts445
10.1002/prot.21655
10.1073/pnas.0509379103
10.1038/nature06522
10.1371/journal.pcbi.1000323
10.1529/biophysj.108.135467
10.1371/journal.pbio.1001193
10.1002/1099-1387(200009)6:9<453::AID-PSC284>3.0.CO;2-Z
10.1016/j.str.2009.06.008
10.1021/bi1007222
10.1016/j.cbpa.2010.07.020
10.1093/bioinformatics/btr168
10.1021/ja060896t
10.1021/ct050307u
10.1038/271618a0
10.1038/nature04105
10.1093/nar/gkh028
10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1
10.1002/prot.20049
10.1093/nar/gkm993
10.1093/bioinformatics/btp304
10.1002/pro.5560030608
10.1093/bioinformatics/btp512
10.1110/ps.04882105
10.1021/jp046736q
10.1038/nsb881
10.1073/pnas.0701393104
10.1073/pnas.1230801100
10.1073/pnas.0605534104
10.1186/1472-6807-10-26
10.1093/bioinformatics/btp339
10.1146/annurev.bi.59.070190.005043
10.1371/journal.pcbi.1002428
10.1038/nrg1672
10.1126/science.7886447
10.1093/nar/26.18.4280
10.1016/S0301-0104(00)00222-6
10.1093/nar/gkr987
10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U
10.1002/j.1460-2075.1986.tb04288.x
10.1126/science.1066176
10.1002/jcc.540161210
ContentType Journal Article
Copyright 2012 Elsevier B.V.
Copyright © 2012 Elsevier B.V. All rights reserved.
Copyright_xml – notice: 2012 Elsevier B.V.
– notice: Copyright © 2012 Elsevier B.V. All rights reserved.
DBID AAYXX
CITATION
CGR
CUY
CVF
ECM
EIF
NPM
7X8
DOI 10.1016/j.plrev.2012.10.009
DatabaseName CrossRef
Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
MEDLINE - Academic
DatabaseTitle CrossRef
MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
MEDLINE - Academic
DatabaseTitleList MEDLINE
MEDLINE - Academic
Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: EIF
  name: MEDLINE
  url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search
  sourceTypes: Index Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 1873-1457
EndPage 26
ExternalDocumentID 23199577
10_1016_j_plrev_2012_10_009
S1571064512001327
Genre Comparative Study
Review
Research Support, Non-U.S. Gov't
Journal Article
GroupedDBID ---
--K
--M
.~1
0R~
123
1B1
1~.
1~5
4.4
457
4G.
53G
5VS
7-5
71M
8P~
AACTN
AAEDT
AAEDW
AAIAV
AAIKJ
AAKOC
AALRI
AAOAW
AAQFI
AAXUO
ABGSF
ABJNI
ABMAC
ABNEU
ABUDA
ABXDB
ABYKQ
ACDAQ
ACFVG
ACGFS
ACNNM
ACRLP
ADBBV
ADEZE
ADMUD
ADUVX
AEBSH
AEHWI
AEKER
AENEX
AFKWA
AFTJW
AFXIZ
AGHFR
AGRDE
AGUBO
AGYEJ
AIEXJ
AIKHN
AITUG
AIVDX
AJBFU
AJOXV
ALMA_UNASSIGNED_HOLDINGS
AMFUW
AMRAJ
AXJTR
BKOJK
BLXMC
CS3
DOVZS
DU5
EBS
EFJIC
EFLBG
EJD
EO8
EO9
EP2
EP3
F5P
FDB
FEDTE
FIRID
FNPLU
FYGXN
G-Q
GBLVA
HVGLF
HZ~
IHE
J1W
KOM
M41
MO0
N9A
O-L
O9-
OAUVE
OGIMB
OZT
P-8
P-9
P2P
PC.
Q38
RIG
ROL
RPZ
SDF
SDG
SES
SEW
SPC
SPCBC
SPD
SSQ
SSU
SSZ
T5K
~G-
AATTM
AAXKI
AAYWO
AAYXX
ABWVN
ACRPL
ACVFH
ADCNI
ADNMO
AEIPS
AEUPX
AFJKZ
AFPUW
AGCQF
AGRNS
AIGII
AIIUN
AKBMS
AKRWK
AKYEP
ANKPU
APXCP
BNPGV
CITATION
SSH
CGR
CUY
CVF
ECM
EIF
NPM
7X8
ID FETCH-LOGICAL-c359t-ffcf438ce429a984b9ef6e9490091aa41822049f809779161c9896b8206991c03
IEDL.DBID .~1
ISSN 1571-0645
1873-1457
IngestDate Fri Jul 11 02:12:40 EDT 2025
Thu Apr 03 07:04:04 EDT 2025
Tue Jul 01 03:19:26 EDT 2025
Thu Apr 24 22:55:46 EDT 2025
Fri Feb 23 02:29:53 EST 2024
IsPeerReviewed true
IsScholarly true
Issue 1
Language English
License https://www.elsevier.com/tdm/userlicense/1.0
Copyright © 2012 Elsevier B.V. All rights reserved.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c359t-ffcf438ce429a984b9ef6e9490091aa41822049f809779161c9896b8206991c03
Notes ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-1
ObjectType-Review-3
content type line 23
PMID 23199577
PQID 1328229076
PQPubID 23479
PageCount 26
ParticipantIDs proquest_miscellaneous_1328229076
pubmed_primary_23199577
crossref_primary_10_1016_j_plrev_2012_10_009
crossref_citationtrail_10_1016_j_plrev_2012_10_009
elsevier_sciencedirect_doi_10_1016_j_plrev_2012_10_009
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate March 2013
2013-03-00
2013-Mar
20130301
PublicationDateYYYYMMDD 2013-03-01
PublicationDate_xml – month: 03
  year: 2013
  text: March 2013
PublicationDecade 2010
PublicationPlace Netherlands
PublicationPlace_xml – name: Netherlands
PublicationTitle Physics of life reviews
PublicationTitleAlternate Phys Life Rev
PublicationYear 2013
Publisher Elsevier B.V
Publisher_xml – name: Elsevier B.V
References Pascual-García, Abia, Ortiz, Bastolla (br1180) 2009; 5
Bavro, De Zorzi, Schmidt, Muniz, Zubcevic, Sansom (br0110) 2012; 19
Zheng, Brooks, Thirumalai (br1770) 2007; 93
Provasi, Artacho, Negri, Mobarec, Filizola (br1290) 2011; 7
Humphrey, Dalke, Schulten (br0680) 1996; 14
Finkelstein (br0420) 2002
Gerstein, Lesk, Chothia (br0490) 1994; 33
Tsutsumi, Mollapour, Graf, Lee, Scroggins, Xu (br1600) 2009; 16
Zheng, Brooks, Doniach, Thirumalai (br1780) 2005; 13
Rueda, Chacón, Orozco (br1400) 2007; 15
Needleman, Wunsch (br1120) 1970; 48
Keskin, Jernigan, Bahar (br0730) 2000; 78
Cascella, Micheletti, Rothlisberger, Carloni (br0220) 2005; 127
Eisenmesser, Millet, Labeikovsky, Korzhnev, Wolf-Watz, Bosco (br0380) 2005; 438
Pontiggia, Colombo, Micheletti, Orland (br1240) 2007; 98
Cascella, Micheletti, Rothlisberger, Carloni (br0210) 2005; 127
Micheletti, Orland (br1000) 2009; 25
Holm, Park (br0650) 2000; 16
Pegg, Brown, Ojha, Seffernick, Meng, Morris (br1200) 2006; 45
Micheletti, Banavar, Maritan (br0970) 2001; 87
Miyashita, Onuchic, Wolynes (br1030) 2003; 100
Pontiggia, Zen, Micheletti (br1250) 2008; 95
Das, Mahale, Prashar, Bihani, Ferrer, Hosur (br0300) 2010; 132
DePristo, Weinreich, Hartl (br0340) 2005; 6
Lesk (br0820) 2004
Williams, Lovell (br1660) 2009; 26
Tama, Sanejouand (br1540) 2001; 14
Teilum, Olsen, Kragelund (br1560) 2009; 66
Henzler-Wildman, Thai, Lei, Ott, Wolf-Watz, Fenn (br0590) 2007; 450
Romo, Grossfield (br1850) 2011; 79
Fanning, Anderson (br0400) 1999; 103
Alexandrov, Lehnert, Echols, Milburn, Engelman, Gerstein (br0040) 2005; 14
Sachs, Engelman (br1860) 2006; 75
Mizuguchi, Deane, Blundell, Overington (br1050) 1998; 7
Hammes-Schiffer, Benkovic (br0530) 2006; 75
Kong, Karplus (br0750) 2009; 74
Mendez, Bastolla (br0950) 2010; 104
del Sol, Tsai, Ma, Nussinov (br0320) 2009; 17
Skolnick, Arakaki, Lee, Brylinski (br1450) 2009; 106
Hinsen, Thomas, Field (br0640) 1999; 34
Janezic, Venable, Brooks (br0710) 1995; 16
Ortiz, Strauss, Olmea (br1160) 2002; 11
Engel, Gaub (br1820) 2008; 77
Zhou, Cook, Karplus (br1800) 2000; 79
Weinreich, Delaney, Depristo, Hartl (br1650) 2006; 312
Zen, de Chiara, Pastore, Micheletti (br1740) 2009; 25
Kitao, Hayward, Go (br0740) 1998; 33
Lockless, Ranganathan (br0860) 1999; 286
Zen, Carnevale, Lesk, Micheletti (br1730) 2008; 17
Zheng, Brooks, Thirumalai (br1790) 2009; 10
Carnevale, Raugei, Micheletti, Carloni (br0200) 2007; 111
Henzler-Wildman, Kern (br0570) 2007; 450
Kurkcuoglu, Jernigan, Doruker (br0780) 2006; 45
Amadei, Ceruso, Di Nola (br0050) 1999; 36
Atilgan, Durell, Jernigan, Demirel, Keskin, Bahar (br0080) 2001; 80
Murzin, Brenner, Hubbard, Chothia (br1100) 1995; 247
Münz, Lyngso, Hein, Biggin (br1090) 2010; 11
Gerstein, Krebs (br0480) 1998; 26
Piana, Carloni, Rothlisberger (br1230) 2002; 11
Smith, Sternberg, Bates (br1460) 2005; 347
Song, Jernigan (br1470) 2006; 63
Porter, Bartlett, Thornton (br1260) 2004; 32
Hinsen, Kneller (br0620) 2008; 70
Capozzi, Luchinat, Micheletti, Pontiggia (br0170) 2007; 6
Morra, Potestio, Micheletti, Colombo (br1060) 2012; 8
Shakhnovich, Deeds, Delisi, Shakhnovich (br1430) 2005; 15
Delarue, Sanejouand (br0330) 2002; 320
Potestio, Aleksiev, Pontiggia, Cozzini, Micheletti (br1270) 2010; 38
Liu, Gronenborn, Bahar (br1840) 2011; 80
Rueda, Ferrer-Costa, Meyer, Pérez, Camps, Hospital (br1410) 2007; 104
Micheletti, Carloni, Maritan (br0990) 2004; 55
Sulkowska, Kloczkowski, Sen, Cieplak, Jernigan (br1530) 2007; 71
Kamath, Howell, Agarwal (br0720) 2010; 49
Holm, Sander (br0660) 1994; 22
Tyndall, Nall, Fairlie (br1610) 2005; 105
Agarwal, Billeter, Rajagopalan, Benkovic, Hammes-Schiffer (br0010) 2002; 99
Bartlett, Borkakoti, Thornton (br0100) 2003; 331
Eisenmesser, Bosco, Akke, Kern (br0370) 2002; 295
Holm, Sander (br0670) 1996; 273
Levy, Srinivasan, Olson, McCammon (br0840) 1984; 23
Amadei, Linssen, Berendsen (br0060) 1993; 17
Quesada, Ordóñez, Sánchez, Puente, López-Otín (br1320) 2009; 37
Yang, Luo, Karnchanaphanurach, Louie, Rech, Cova (br1690) 2003; 302
Fuglebakk, Echave, Reuter (br0460) 2012
Hinsen, Petrescu, Dellerue, Bellisent-Funel, Kneller (br0630) 2000; 261
Orellana, Rueda, Ferrer-Costa, Lopez-Blanco, Chacon, Orozco (br0790) 2010; 6
Maguid, Fernandez-Alberti, Ferrelli, Echave (br0900) 2005; 89
Ojha, Meng, Babbitt (br1130) 2007; 3
Pearl, Todd, Sillitoe, Dibley, Redfern, Lewis (br1190) 2005; 33
Echave (br0350) 2012; 84
Ramanathan, Savol, Langmead, Agarwal, Chennubhotla (br1350) 2011; 6
Frauenfelder, Sligar, Wolynes (br0450) 1991; 254
Lopéz-Blanco, Garzón, Chacón (br0870) 2011; 27
Yesylevskyy, Kharkyanen, Demchenko (br1710) 2006; 119
Fleming, Kelley, Islam, MacCallum, Muller, Pazos (br0430) 2006; 361
Bakan, Meireles, Bahar (br1810) 2011; 27
Potestio, Pontiggia, Micheletti (br1280) 2009; 96
Golhlke, Thorpe (br0520) 2006; 91
Micheletti, Banavar, Maritan, Seno (br0980) 1999; 82
Rawlings, Barrett, Bateman (br1370) 2012; 40
Suel, Lockless, Wall, Ranganathan (br1520) 2003; 10
McCammon, Gelin, Karplus, Wolynes (br0940) 1976; 262
Zhang, Hubner, Arakaki, Shakhnovich, Skolnick (br1760) 2006; 103
Maguid, Fernandez-Alberti, Echave (br0890) 2008; 422
Velázquez-Muriel, Rueda, Cuesta, Pascual-Montano, Orozco, Carazo (br1630) 2009; 9
Frauenfelder, Parak, Young (br0440) 1988; 17
Hinsen (br0610) 1998; 33
Morra, Verkhivker, Colombo (br1070) 2009; 5
Chothia (br0260) 1992; 357
Gerek, Ozkan (br1830) 2011; 7
Janezic, Brooks (br0700) 1995; 16
Vasko, Rodriguez, Cunningham, Ardi, Agard, McAlpine (br1620) 2010; 1
Hayward, Kitao, Berendsen (br0540) 1997; 27
Wolynes, Onuchic, Thirumalai (br1670) 1995; 267
Xie, Bourne (br1680) 2008; 105
Brooks, Janezic, Karplus (br0150) 1995; 16
Henzler-Wildman, Lei, Thai, Kerns, Karplus, Kern (br0580) 2007; 450
Leo-Macias, Lopez-Romero, Lupyan, Zerbino, Ortiz (br0810) 2005; 88
Echave, Fernández (br0360) 2010; 78
Stebbings, Mizuguchi (br1500) 2004; 32
Ye, Godzik (br1700) 2004; 32
Maritan, Micheletti, Trovato, Banavar (br0930) 2000; 406
Pang, Arinaminpathy, Sansom, Biggin (br1170) 2005; 61
Camps, Carrillo, Emperador, Orellana, Hospital, Rueda (br0160) 2009; 25
Thompson, Gibson, Plewniak, Jeanmougin, Higgins (br1570) 1997; 25
Meyerguz, Kleinberg, Elber (br0960) 2007; 104
Miyashita, Wolynes, Onuchic (br1040) 2005; 109
Tobi (br1590) 2012; 80
Stein, Rueda, Panjkovich, Orozco, Aloy (br1510) 2011; 19
Bahar, Atilgan, Erman (br0090) 1997; 2
Fersht (br0410) 1999
Orengo, Thornton (br1140) 2005; 74
De los Rios, Cecconi, Pretre, Dietler, Michielin, Piazza (br0310) 2005; 89
Glembo, Farrell, Gerek, Thorpe, Ozkan (br0500) 2012; 8
Rod, Radkiewicz, Brooks (br1380) 2003; 100
Zen, Micheletti, Keskin, Nussinov (br1750) 2010; 10
Chandonia, Hon, Walker, Lo Conte, Koehl, Levitt (br0230) 2004; 32
Kundu, Sorensen, Phillips (br0770) 2004; 57
Boehr, Dyson, Wright (br0140) 2008; 47
Lu, Poon, Ma (br0880) 2006; 2
Ranea, Sillero, Thornton, Orengo (br1360) 2006; 63
Ming, Wall (br1020) 2005; 95
Chennubhotla, Bahar (br0240) 2007; 3
Pugalenthi, Bhaduri, Sowdhamini (br1300) 2005; 33
Blundell, Srinivasan (br0130) 1996; 93
Chi, Elfström, Shi, Snäll, Engström, Jemth (br0250) 2008; 105
Tirion (br1580) 1996; 77
Nashine, Hammes-Schiffer, Benkovic (br1110) 2010; 14
Orozco, Orellana, Hospital, Naganathan, Emperador, Carrillo (br1150) 2011; 85
Creighton (br0290) 1993
Münz, Hein, Biggin (br1080) 2012; 8
Zeldovich, Shakhnovich (br1720) 2008; 59
Krebs, Alexandrov, Wilson, Echols, Yu, Gerstein (br0760) 2002; 48
Bhabha, Lee, Ekiert, Gam, Wilson, Dyson (br0120) 2011; 332
Maguid, Fernández-Alberti, Parisi, Echave (br0910) 2006; 63
Hess (br0600) 2002; 65
Min, Luo, Cherayil, Kou, Xie (br1010) 2005; 94
Pérez, Blas, Rueda, López-Bes, de la Cruz, Orozco (br1310) 2005; 1
Carnevale, Raugei, Micheletti, Carloni (br0190) 2006; 128
Ramanathan, Agarwal (br1340) 2011; 9
Vishveshwara, Ghosh, Hansia (br1640) 2009; 10
Hayward, Kitao, Go (br0550) 1994; 3
Falke (br0390) 2002; 295
Radkiewicz, Zipse, Clarke, Houk (br1330) 2001; 123
Chothia, Lesk (br0280) 1986; 5
Jackson, Foo, Tokuriki, Afriat, Carr, Kim (br0690) 2009; 106
Garcia (br0470) 1992; 68
Hensen, Meyer, Haas, Rex, Vriend, Grubmüller (br0560) 2012; 7
Andreeva, Howorth, Chandonia, Brenner, Hubbard, Chothia (br0070) 2008; 36
Sacquin-Mora, Laforet, Lavery (br1420) 2007; 67
Songyang, Fanning, Fu, Xu, Marfatia, Chishti (br1480) 1997; 275
Shatsky, Nussinov, Wolfson (br1440) 2004; 56
Levitt, Sander, Stern (br0830) 1985; 181
Aleksiev, Potestio, Pontiggia, Cozzini, Micheletti (br0030) 2009; 25
Carnevale, Pontiggia, Micheletti (br0180) 2007; 19
Perryman, Lin, McCammon (br1210) 2004; 13
Southan (br1490) 2000; 6
Tang, James, Hsu, Jenkins, Blundell (br1550) 1978; 271
Go, Noguti, Nishikawa (br0510) 1983; 80
Piana, Carloni, Parrinello (br1220) 2002; 319
Law, Fuentes, Lee (br0800) 2009; 131
Liu, Bahar (br0850) 2012; 29
Maritan, Micheletti, Banavar (br0920) 2000; 84
Chothia, Finkelstein (br0270) 1990; 59
Piana (10.1016/j.plrev.2012.10.009_br1230) 2002; 11
Liu (10.1016/j.plrev.2012.10.009_br0850) 2012; 29
Lu (10.1016/j.plrev.2012.10.009_br0880) 2006; 2
Hammes-Schiffer (10.1016/j.plrev.2012.10.009_br0530) 2006; 75
Pugalenthi (10.1016/j.plrev.2012.10.009_br1300) 2005; 33
Orengo (10.1016/j.plrev.2012.10.009_br1140) 2005; 74
Zheng (10.1016/j.plrev.2012.10.009_br1770) 2007; 93
Carnevale (10.1016/j.plrev.2012.10.009_br0180) 2007; 19
Zen (10.1016/j.plrev.2012.10.009_br1740) 2009; 25
Shakhnovich (10.1016/j.plrev.2012.10.009_br1430) 2005; 15
Fersht (10.1016/j.plrev.2012.10.009_br0410) 1999
Skolnick (10.1016/j.plrev.2012.10.009_br1450) 2009; 106
Chi (10.1016/j.plrev.2012.10.009_br0250) 2008; 105
Sachs (10.1016/j.plrev.2012.10.009_br1860) 2006; 75
Suel (10.1016/j.plrev.2012.10.009_br1520) 2003; 10
Cascella (10.1016/j.plrev.2012.10.009_br0210) 2005; 127
Cascella (10.1016/j.plrev.2012.10.009_br0220) 2005; 127
Echave (10.1016/j.plrev.2012.10.009_br0350) 2012; 84
Micheletti (10.1016/j.plrev.2012.10.009_br1000) 2009; 25
Münz (10.1016/j.plrev.2012.10.009_br1090) 2010; 11
Shatsky (10.1016/j.plrev.2012.10.009_br1440) 2004; 56
Hayward (10.1016/j.plrev.2012.10.009_br0540) 1997; 27
Pontiggia (10.1016/j.plrev.2012.10.009_br1250) 2008; 95
Micheletti (10.1016/j.plrev.2012.10.009_br0980) 1999; 82
Xie (10.1016/j.plrev.2012.10.009_br1680) 2008; 105
Southan (10.1016/j.plrev.2012.10.009_br1490) 2000; 6
Chothia (10.1016/j.plrev.2012.10.009_br0280) 1986; 5
Camps (10.1016/j.plrev.2012.10.009_br0160) 2009; 25
Das (10.1016/j.plrev.2012.10.009_br0300) 2010; 132
Hess (10.1016/j.plrev.2012.10.009_br0600) 2002; 65
Micheletti (10.1016/j.plrev.2012.10.009_br0970) 2001; 87
Zhang (10.1016/j.plrev.2012.10.009_br1760) 2006; 103
Janezic (10.1016/j.plrev.2012.10.009_br0710) 1995; 16
Alexandrov (10.1016/j.plrev.2012.10.009_br0040) 2005; 14
Leo-Macias (10.1016/j.plrev.2012.10.009_br0810) 2005; 88
Capozzi (10.1016/j.plrev.2012.10.009_br0170) 2007; 6
Delarue (10.1016/j.plrev.2012.10.009_br0330) 2002; 320
Murzin (10.1016/j.plrev.2012.10.009_br1100) 1995; 247
Zhou (10.1016/j.plrev.2012.10.009_br1800) 2000; 79
Andreeva (10.1016/j.plrev.2012.10.009_br0070) 2008; 36
Bavro (10.1016/j.plrev.2012.10.009_br0110) 2012; 19
DePristo (10.1016/j.plrev.2012.10.009_br0340) 2005; 6
Hinsen (10.1016/j.plrev.2012.10.009_br0630) 2000; 261
Pang (10.1016/j.plrev.2012.10.009_br1170) 2005; 61
Ojha (10.1016/j.plrev.2012.10.009_br1130) 2007; 3
Wolynes (10.1016/j.plrev.2012.10.009_br1670) 1995; 267
Kong (10.1016/j.plrev.2012.10.009_br0750) 2009; 74
Henzler-Wildman (10.1016/j.plrev.2012.10.009_br0580) 2007; 450
Lesk (10.1016/j.plrev.2012.10.009_br0820) 2004
Rod (10.1016/j.plrev.2012.10.009_br1380) 2003; 100
Creighton (10.1016/j.plrev.2012.10.009_br0290) 1993
Henzler-Wildman (10.1016/j.plrev.2012.10.009_br0590) 2007; 450
Orozco (10.1016/j.plrev.2012.10.009_br1150) 2011; 85
Law (10.1016/j.plrev.2012.10.009_br0800) 2009; 131
Maguid (10.1016/j.plrev.2012.10.009_br0890) 2008; 422
Velázquez-Muriel (10.1016/j.plrev.2012.10.009_br1630) 2009; 9
Nashine (10.1016/j.plrev.2012.10.009_br1110) 2010; 14
Chandonia (10.1016/j.plrev.2012.10.009_br0230) 2004; 32
Henzler-Wildman (10.1016/j.plrev.2012.10.009_br0570) 2007; 450
Lopéz-Blanco (10.1016/j.plrev.2012.10.009_br0870) 2011; 27
Zen (10.1016/j.plrev.2012.10.009_br1730) 2008; 17
Humphrey (10.1016/j.plrev.2012.10.009_br0680) 1996; 14
Keskin (10.1016/j.plrev.2012.10.009_br0730) 2000; 78
Ortiz (10.1016/j.plrev.2012.10.009_br1160) 2002; 11
Potestio (10.1016/j.plrev.2012.10.009_br1280) 2009; 96
Rueda (10.1016/j.plrev.2012.10.009_br1400) 2007; 15
Tyndall (10.1016/j.plrev.2012.10.009_br1610) 2005; 105
Bhabha (10.1016/j.plrev.2012.10.009_br0120) 2011; 332
Songyang (10.1016/j.plrev.2012.10.009_br1480) 1997; 275
Tirion (10.1016/j.plrev.2012.10.009_br1580) 1996; 77
Tsutsumi (10.1016/j.plrev.2012.10.009_br1600) 2009; 16
Bartlett (10.1016/j.plrev.2012.10.009_br0100) 2003; 331
Stebbings (10.1016/j.plrev.2012.10.009_br1500) 2004; 32
Thompson (10.1016/j.plrev.2012.10.009_br1570) 1997; 25
Carnevale (10.1016/j.plrev.2012.10.009_br0190) 2006; 128
Eisenmesser (10.1016/j.plrev.2012.10.009_br0380) 2005; 438
Kitao (10.1016/j.plrev.2012.10.009_br0740) 1998; 33
Quesada (10.1016/j.plrev.2012.10.009_br1320) 2009; 37
Amadei (10.1016/j.plrev.2012.10.009_br0050) 1999; 36
Smith (10.1016/j.plrev.2012.10.009_br1460) 2005; 347
Vishveshwara (10.1016/j.plrev.2012.10.009_br1640) 2009; 10
Ramanathan (10.1016/j.plrev.2012.10.009_br1350) 2011; 6
Hayward (10.1016/j.plrev.2012.10.009_br0550) 1994; 3
Orellana (10.1016/j.plrev.2012.10.009_br0790) 2010; 6
Frauenfelder (10.1016/j.plrev.2012.10.009_br0450) 1991; 254
Maguid (10.1016/j.plrev.2012.10.009_br0910) 2006; 63
Maritan (10.1016/j.plrev.2012.10.009_br0930) 2000; 406
Tang (10.1016/j.plrev.2012.10.009_br1550) 1978; 271
Frauenfelder (10.1016/j.plrev.2012.10.009_br0440) 1988; 17
Kurkcuoglu (10.1016/j.plrev.2012.10.009_br0780) 2006; 45
Golhlke (10.1016/j.plrev.2012.10.009_br0520) 2006; 91
Micheletti (10.1016/j.plrev.2012.10.009_br0990) 2004; 55
Janezic (10.1016/j.plrev.2012.10.009_br0700) 1995; 16
Zeldovich (10.1016/j.plrev.2012.10.009_br1720) 2008; 59
Garcia (10.1016/j.plrev.2012.10.009_br0470) 1992; 68
Ranea (10.1016/j.plrev.2012.10.009_br1360) 2006; 63
Romo (10.1016/j.plrev.2012.10.009_br1850) 2011; 79
Zen (10.1016/j.plrev.2012.10.009_br1750) 2010; 10
Provasi (10.1016/j.plrev.2012.10.009_br1290) 2011; 7
Ramanathan (10.1016/j.plrev.2012.10.009_br1340) 2011; 9
Chothia (10.1016/j.plrev.2012.10.009_br0260) 1992; 357
Radkiewicz (10.1016/j.plrev.2012.10.009_br1330) 2001; 123
Kundu (10.1016/j.plrev.2012.10.009_br0770) 2004; 57
Hensen (10.1016/j.plrev.2012.10.009_br0560) 2012; 7
Lockless (10.1016/j.plrev.2012.10.009_br0860) 1999; 286
Miyashita (10.1016/j.plrev.2012.10.009_br1030) 2003; 100
Morra (10.1016/j.plrev.2012.10.009_br1060) 2012; 8
Fleming (10.1016/j.plrev.2012.10.009_br0430) 2006; 361
Levy (10.1016/j.plrev.2012.10.009_br0840) 1984; 23
Maritan (10.1016/j.plrev.2012.10.009_br0920) 2000; 84
Morra (10.1016/j.plrev.2012.10.009_br1070) 2009; 5
Yesylevskyy (10.1016/j.plrev.2012.10.009_br1710) 2006; 119
Levitt (10.1016/j.plrev.2012.10.009_br0830) 1985; 181
Ming (10.1016/j.plrev.2012.10.009_br1020) 2005; 95
Perryman (10.1016/j.plrev.2012.10.009_br1210) 2004; 13
Song (10.1016/j.plrev.2012.10.009_br1470) 2006; 63
Miyashita (10.1016/j.plrev.2012.10.009_br1040) 2005; 109
Holm (10.1016/j.plrev.2012.10.009_br0650) 2000; 16
Boehr (10.1016/j.plrev.2012.10.009_br0140) 2008; 47
Krebs (10.1016/j.plrev.2012.10.009_br0760) 2002; 48
Stein (10.1016/j.plrev.2012.10.009_br1510) 2011; 19
Zheng (10.1016/j.plrev.2012.10.009_br1790) 2009; 10
Holm (10.1016/j.plrev.2012.10.009_br0660) 1994; 22
Pascual-García (10.1016/j.plrev.2012.10.009_br1180) 2009; 5
Eisenmesser (10.1016/j.plrev.2012.10.009_br0370) 2002; 295
Piana (10.1016/j.plrev.2012.10.009_br1220) 2002; 319
Engel (10.1016/j.plrev.2012.10.009_br1820) 2008; 77
Fuglebakk (10.1016/j.plrev.2012.10.009_br0460) 2012
Glembo (10.1016/j.plrev.2012.10.009_br0500) 2012; 8
Jackson (10.1016/j.plrev.2012.10.009_br0690) 2009; 106
De los Rios (10.1016/j.plrev.2012.10.009_br0310) 2005; 89
Chennubhotla (10.1016/j.plrev.2012.10.009_br0240) 2007; 3
Rawlings (10.1016/j.plrev.2012.10.009_br1370) 2012; 40
Yang (10.1016/j.plrev.2012.10.009_br1690) 2003; 302
Needleman (10.1016/j.plrev.2012.10.009_br1120) 1970; 48
Pontiggia (10.1016/j.plrev.2012.10.009_br1240) 2007; 98
del Sol (10.1016/j.plrev.2012.10.009_br0320) 2009; 17
Go (10.1016/j.plrev.2012.10.009_br0510) 1983; 80
Mizuguchi (10.1016/j.plrev.2012.10.009_br1050) 1998; 7
Rueda (10.1016/j.plrev.2012.10.009_br1410) 2007; 104
Blundell (10.1016/j.plrev.2012.10.009_br0130) 1996; 93
Pérez (10.1016/j.plrev.2012.10.009_br1310) 2005; 1
Atilgan (10.1016/j.plrev.2012.10.009_br0080) 2001; 80
Sulkowska (10.1016/j.plrev.2012.10.009_br1530) 2007; 71
Aleksiev (10.1016/j.plrev.2012.10.009_br0030) 2009; 25
Mendez (10.1016/j.plrev.2012.10.009_br0950) 2010; 104
McCammon (10.1016/j.plrev.2012.10.009_br0940) 1976; 262
Potestio (10.1016/j.plrev.2012.10.009_br1270) 2010; 38
Liu (10.1016/j.plrev.2012.10.009_br1840) 2011; 80
Pearl (10.1016/j.plrev.2012.10.009_br1190) 2005; 33
Pegg (10.1016/j.plrev.2012.10.009_br1200) 2006; 45
Bahar (10.1016/j.plrev.2012.10.009_br0090) 1997; 2
Sacquin-Mora (10.1016/j.plrev.2012.10.009_br1420) 2007; 67
Porter (10.1016/j.plrev.2012.10.009_br1260) 2004; 32
Williams (10.1016/j.plrev.2012.10.009_br1660) 2009; 26
Teilum (10.1016/j.plrev.2012.10.009_br1560) 2009; 66
Hinsen (10.1016/j.plrev.2012.10.009_br0640) 1999; 34
Maguid (10.1016/j.plrev.2012.10.009_br0900) 2005; 89
Hinsen (10.1016/j.plrev.2012.10.009_br0610) 1998; 33
Tama (10.1016/j.plrev.2012.10.009_br1540) 2001; 14
Ye (10.1016/j.plrev.2012.10.009_br1700) 2004; 32
Münz (10.1016/j.plrev.2012.10.009_br1080) 2012; 8
Holm (10.1016/j.plrev.2012.10.009_br0670) 1996; 273
Fanning (10.1016/j.plrev.2012.10.009_br0400) 1999; 103
Zheng (10.1016/j.plrev.2012.10.009_br1780) 2005; 13
Tobi (10.1016/j.plrev.2012.10.009_br1590) 2012; 80
Gerek (10.1016/j.plrev.2012.10.009_br1830) 2011; 7
Min (10.1016/j.plrev.2012.10.009_br1010) 2005; 94
Kamath (10.1016/j.plrev.2012.10.009_br0720) 2010; 49
Vasko (10.1016/j.plrev.2012.10.009_br1620) 2010; 1
Weinreich (10.1016/j.plrev.2012.10.009_br1650) 2006; 312
Falke (10.1016/j.plrev.2012.10.009_br0390) 2002; 295
Gerstein (10.1016/j.plrev.2012.10.009_br0480) 1998; 26
Hinsen (10.1016/j.plrev.2012.10.009_br0620) 2008; 70
Bakan (10.1016/j.plrev.2012.10.009_br1810) 2011; 27
Finkelstein (10.1016/j.plrev.2012.10.009_br0420) 2002
Chothia (10.1016/j.plrev.2012.10.009_br0270) 1990; 59
Echave (10.1016/j.plrev.2012.10.009_br0360) 2010; 78
Meyerguz (10.1016/j.plrev.2012.10.009_br0960) 2007; 104
Agarwal (10.1016/j.plrev.2012.10.009_br0010) 2002; 99
Amadei (10.1016/j.plrev.2012.10.009_br0060) 1993; 17
Carnevale (10.1016/j.plrev.2012.10.009_br0200) 2007; 111
Gerstein (10.1016/j.plrev.2012.10.009_br0490) 1994; 33
Brooks (10.1016/j.plrev.2012.10.009_br0150) 1995; 16
23154221 - Phys Life Rev. 2013 Mar;10(1):29-30; discussion 39-40
23154220 - Phys Life Rev. 2013 Mar;10(1):33-4; discussion 39-40
23394959 - Phys Life Rev. 2013 Mar;10(1):37-8; discussion 39-40
23157841 - Phys Life Rev. 2013 Mar;10(1):35-6; discussion 39-40
23141839 - Phys Life Rev. 2013 Mar;10(1):31-2; discussion 39-40
23122425 - Phys Life Rev. 2013 Mar;10(1):27-8; discussion 39-40
References_xml – volume: 9
  start-page: 6
  year: 2009
  ident: br1630
  article-title: Comparison of molecular dynamics and superfamily spaces of protein domain deformation
  publication-title: BMC Struct Biol
– volume: 254
  start-page: 1598
  year: 1991
  end-page: 1603
  ident: br0450
  article-title: The energy landscapes and motions of proteins
  publication-title: Science
– volume: 63
  start-page: 513
  year: 2006
  end-page: 525
  ident: br1360
  article-title: Protein superfamily evolution and the last universal common ancestor (LUCA)
  publication-title: J Mol Evol
– volume: 23
  start-page: 1099
  year: 1984
  end-page: 1112
  ident: br0840
  article-title: Quasi-harmonic method for studying very low frequency modes in proteins
  publication-title: Biopolymers
– volume: 247
  start-page: 536
  year: 1995
  end-page: 540
  ident: br1100
  article-title: SCOP: a structural classification of proteins database for the investigation of sequences and structures
  publication-title: J Mol Biol
– volume: 6
  start-page: 678
  year: 2005
  end-page: 687
  ident: br0340
  article-title: Missense meanderings in sequence space: a biophysical view of protein evolution
  publication-title: Nat Rev Genet
– volume: 132
  start-page: 6366
  year: 2010
  end-page: 6373
  ident: br0300
  article-title: X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate
  publication-title: J Am Chem Soc
– volume: 16
  start-page: 1543
  year: 1995
  end-page: 1553
  ident: br0700
  article-title: Harmonic analysis of large systems ii. comparison of different protein models
  publication-title: J Comput Chem
– volume: 7
  start-page: e1002154
  year: 2011
  ident: br1830
  article-title: Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning
  publication-title: PLoS Comput Biol
– volume: 105
  start-page: 5441
  year: 2008
  end-page: 5446
  ident: br1680
  article-title: Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
  publication-title: Proc Natl Acad Sci USA
– volume: 71
  start-page: 45
  year: 2007
  end-page: 60
  ident: br1530
  article-title: Predicting the order in which contacts are broken during single molecule protein stretching experiments
  publication-title: Proteins
– volume: 450
  start-page: 964
  year: 2007
  end-page: 972
  ident: br0570
  article-title: Dynamic personalities of proteins
  publication-title: Nature
– volume: 6
  start-page: e15827
  year: 2011
  ident: br1350
  article-title: Discovering conformational sub-states relevant to protein function
  publication-title: PLoS ONE
– volume: 438
  start-page: 117
  year: 2005
  end-page: 121
  ident: br0380
  article-title: Intrinsic dynamics of an enzyme underlies catalysis
  publication-title: Nature
– volume: 16
  start-page: 566
  year: 2000
  end-page: 567
  ident: br0650
  article-title: Dalilite workbench for protein structure comparison
  publication-title: Bioinformatics
– volume: 78
  start-page: 173
  year: 2010
  end-page: 180
  ident: br0360
  article-title: A perturbative view of protein structural variation
  publication-title: Proteins
– volume: 66
  start-page: 2231
  year: 2009
  end-page: 2247
  ident: br1560
  article-title: Functional aspects of protein flexibility
  publication-title: Cell Mol Life Sci
– volume: 74
  start-page: 867
  year: 2005
  end-page: 900
  ident: br1140
  article-title: Protein families and their evolution—a structural perspective
  publication-title: Annu Rev Biochem
– volume: 26
  start-page: 4280
  year: 1998
  end-page: 4290
  ident: br0480
  article-title: A database of macromolecular motions
  publication-title: Nucleic Acids Res
– volume: 7
  start-page: 2469
  year: 1998
  end-page: 2471
  ident: br1050
  article-title: HOMSTRAD: a database of protein structure alignments for homologous families
  publication-title: Protein Sci
– volume: 32
  start-page: 189
  year: 2004
  end-page: 192
  ident: br0230
  article-title: The astral compendium in 2004
  publication-title: Nucleic Acids Res
– volume: 119
  start-page: 84
  year: 2006
  end-page: 93
  ident: br1710
  article-title: Hierarchical clustering of correlation patterns: new method of domain identification in proteins
  publication-title: Biophys Chem
– volume: 95
  start-page: 5901
  year: 2008
  end-page: 5912
  ident: br1250
  article-title: Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics
  publication-title: Biophys J
– volume: 96
  start-page: 4993
  year: 2009
  end-page: 5002
  ident: br1280
  article-title: Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits
  publication-title: Biophys J
– volume: 103
  start-page: 2605
  year: 2006
  end-page: 2610
  ident: br1760
  article-title: On the origin and highly likely completeness of single-domain protein structures
  publication-title: Proc Natl Acad Sci USA
– volume: 34
  start-page: 369
  year: 1999
  end-page: 382
  ident: br0640
  article-title: Analysis of domain motion in large proteins
  publication-title: Proteins
– year: 1993
  ident: br0290
  article-title: Proteins, structure and molecular properties
– volume: 49
  start-page: 9078
  year: 2010
  end-page: 9088
  ident: br0720
  article-title: The tail wagging the dog: insights into catalysis in R67 dihydrofolate reductase
  publication-title: Biochemistry
– year: 2004
  ident: br0820
  article-title: Introduction to protein science: architecture, function and genomics
– volume: 273
  start-page: 595
  year: 1996
  end-page: 603
  ident: br0670
  article-title: Mapping the protein universe
  publication-title: Science
– volume: 5
  start-page: e1000323
  year: 2009
  ident: br1070
  article-title: Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
  publication-title: PLoS Comput Biol
– volume: 127
  start-page: 3734
  year: 2005
  end-page: 3742
  ident: br0210
  article-title: Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
  publication-title: J Am Chem Soc
– volume: 103
  start-page: 767
  year: 1999
  end-page: 772
  ident: br0400
  article-title: PDZ domains: fundamental building blocks in the organization of protein complexes at the plasma membrane
  publication-title: J Clin Invest
– volume: 94
  start-page: 198302
  year: 2005
  ident: br1010
  article-title: Observation of a power-law memory kernel for fluctuations within a single protein molecule
  publication-title: Phys Rev Lett
– volume: 36
  start-page: 419
  year: 2008
  end-page: 425
  ident: br0070
  article-title: Data growth and its impact on the SCOP database: new developments
  publication-title: Nucleic Acids Res
– volume: 14
  start-page: 1
  year: 2001
  end-page: 6
  ident: br1540
  article-title: Conformational change of proteins arising from normal mode calculations
  publication-title: Protein Eng
– volume: 93
  start-page: 2289
  year: 2007
  end-page: 2299
  ident: br1770
  article-title: Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations
  publication-title: Biophys J
– volume: 295
  start-page: 1520
  year: 2002
  end-page: 1523
  ident: br0370
  article-title: Enzyme dynamics during catalysis
  publication-title: Science
– volume: 2
  start-page: 464
  year: 2006
  end-page: 471
  ident: br0880
  article-title: A new method for coarse-grained elastic normal-mode analysis
  publication-title: J Chem Theory Comput
– volume: 63
  start-page: 197
  year: 2006
  end-page: 209
  ident: br1470
  article-title: An enhanced elastic network model to represent the motions of domain-swapped proteins
  publication-title: Proteins
– volume: 361
  start-page: 441
  year: 2006
  end-page: 451
  ident: br0430
  article-title: The proteome: structure, function and evolution
  publication-title: Philos Trans R Soc Lond B Biol Sci
– volume: 319
  start-page: 567
  year: 2002
  end-page: 583
  ident: br1220
  article-title: Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
  publication-title: J Mol Biol
– volume: 16
  start-page: 1522
  year: 1995
  end-page: 1542
  ident: br0150
  article-title: Harmonic analysis of large systems I. Methodology
  publication-title: J Comput Chem
– volume: 8
  start-page: e1002749
  year: 2012
  ident: br1080
  article-title: The role of flexibility and conformational selection in the binding promiscuity of PDZ domains
  publication-title: PLoS Comput Biol
– volume: 347
  start-page: 1077
  year: 2005
  end-page: 1101
  ident: br1460
  article-title: The relationship between the flexibility of proteins and their conformational states on forming protein–protein complexes with an application to protein–protein docking
  publication-title: J Mol Biol
– volume: 38
  start-page: 41
  year: 2010
  end-page: 45
  ident: br1270
  article-title: Aladyn: a web server for aligning proteins by matching their large-scale motion
  publication-title: Nucleic Acids Res
– year: 2012
  ident: br0460
  article-title: Measuring and comparing structural fluctuation patterns in large protein datasets
  publication-title: Bioinformatics
– volume: 10
  start-page: 146
  year: 2009
  end-page: 160
  ident: br1640
  article-title: Intra and inter-molecular communications through protein structure network
  publication-title: Curr Protein Pept Sci
– volume: 27
  start-page: 425
  year: 1997
  end-page: 437
  ident: br0540
  article-title: Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme
  publication-title: Proteins
– volume: 32
  start-page: D129
  year: 2004
  end-page: D133
  ident: br1260
  article-title: The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data
  publication-title: Nucl Acids Res
– volume: 80
  start-page: 505
  year: 2001
  end-page: 515
  ident: br0080
  article-title: Anisotropy of fluctuation dynamics of proteins with an elastic network model
  publication-title: Biophys J
– volume: 27
  start-page: 2843
  year: 2011
  end-page: 2850
  ident: br0870
  article-title: iMod: multipurpose normal mode analysis in internal coordinates
  publication-title: Bioinformatics
– volume: 33
  start-page: D247
  year: 2005
  end-page: D251
  ident: br1190
  article-title: The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
  publication-title: Nucl Acids Res
– volume: 16
  start-page: 1544
  year: 1995
  end-page: 1556
  ident: br0710
  article-title: Harmonic analysis of large systems III. Comparison with molecular dynamics
  publication-title: J Comput Chem
– volume: 5
  start-page: e1000331
  year: 2009
  ident: br1180
  article-title: Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures
  publication-title: PLoS Comput Biol
– volume: 33
  start-page: 417
  year: 1998
  end-page: 429
  ident: br0610
  article-title: Analysis of domain motions by approximate normal mode calculations
  publication-title: Proteins
– volume: 8
  year: 2012
  ident: br1060
  article-title: Corresponding functional dynamics across the Hsp90 chaperone family: insights from a multiscale analysis of MD simulations
  publication-title: PLoS Comput Biol
– volume: 331
  start-page: 829
  year: 2003
  end-page: 860
  ident: br0100
  article-title: Catalysing new reactions during evolution: economy of residues and mechanism
  publication-title: J Mol Biol
– volume: 6
  start-page: 4245
  year: 2007
  end-page: 4255
  ident: br0170
  article-title: Essential dynamics of helices provide a functional classification of EF-hand proteins
  publication-title: J Proteome Res
– volume: 77
  start-page: 1905
  year: 1996
  end-page: 1908
  ident: br1580
  article-title: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
  publication-title: Phys Rev Lett
– volume: 17
  start-page: 412
  year: 1993
  end-page: 425
  ident: br0060
  article-title: Essential dynamics of proteins
  publication-title: Proteins
– volume: 84
  start-page: 3009
  year: 2000
  end-page: 3012
  ident: br0920
  article-title: Role of secondary motifs in fast folding polymers: a dynamical variational principle
  publication-title: Phys Rev Lett
– volume: 10
  start-page: 128
  year: 2009
  end-page: 132
  ident: br1790
  article-title: Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks
  publication-title: Curr Protein Pept Sci
– volume: 27
  start-page: 1575
  year: 2011
  end-page: 1577
  ident: br1810
  article-title: Prody: protein dynamics inferred from theory and experiments
  publication-title: Bioinformatics
– volume: 100
  start-page: 12570
  year: 2003
  end-page: 12575
  ident: br1030
  article-title: Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
  publication-title: Proc Natl Acad Sci USA
– volume: 15
  start-page: 385
  year: 2005
  end-page: 392
  ident: br1430
  article-title: Protein structure and evolutionary history determine sequence space topology
  publication-title: Genome Res
– year: 1999
  ident: br0410
  article-title: Structure and mechanism in protein science: a guide to enzyme catalysis and protein folding
– volume: 75
  start-page: 519
  year: 2006
  end-page: 541
  ident: br0530
  article-title: Relating protein motion to catalysis
  publication-title: Annu Rev Biochem
– volume: 123
  start-page: 3499
  year: 2001
  end-page: 3506
  ident: br1330
  article-title: Neighboring side chain effects on asparaginyl and aspartyl degradation: an ab initio study of the relationship between peptide conformation and backbone NH acidity
  publication-title: J Am Chem Soc
– volume: 37
  start-page: 239
  year: 2009
  end-page: 243
  ident: br1320
  article-title: The Degradome database: mammalian proteases and diseases of proteolysis
  publication-title: Nucleic Acids Res
– volume: 14
  start-page: 644
  year: 2010
  end-page: 651
  ident: br1110
  article-title: Coupled motions in enzyme catalysis
  publication-title: Curr Opin Chem Biol
– volume: 45
  start-page: 2545
  year: 2006
  end-page: 2555
  ident: br1200
  article-title: Leveraging enzyme structure–function relationships for functional inference and experimental design: the structure–function linkage database
  publication-title: Biochemistry
– volume: 93
  start-page: 14243
  year: 1996
  end-page: 14248
  ident: br0130
  article-title: Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
  publication-title: Proc Natl Acad Sci USA
– volume: 11
  start-page: 188
  year: 2010
  ident: br1090
  article-title: Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
  publication-title: BMC Bioinform
– volume: 11
  start-page: 2393
  year: 2002
  end-page: 2402
  ident: br1230
  article-title: Drug resistance in HIV-1 protease: flexibility-assisted mechanism of compensatory mutations
  publication-title: Protein Sci
– volume: 11
  start-page: 2606
  year: 2002
  end-page: 2621
  ident: br1160
  article-title: Mammoth (matching molecular models obtained from theory): an automated method for model comparison
  publication-title: Protein Sci
– volume: 17
  start-page: 1042
  year: 2009
  end-page: 1050
  ident: br0320
  article-title: The origin of allosteric functional modulation: multiple pre-existing pathways
  publication-title: Structure
– volume: 79
  start-page: 2902
  year: 2000
  end-page: 2908
  ident: br1800
  article-title: Protein motions at zero-total angular momentum: the importance of long-range correlations
  publication-title: Biophys J
– volume: 127
  start-page: 3734
  year: 2005
  end-page: 3742
  ident: br0220
  article-title: Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
  publication-title: J Am Chem Soc
– volume: 312
  start-page: 111
  year: 2006
  end-page: 114
  ident: br1650
  article-title: Darwinian evolution can follow only very few mutational paths to fitter proteins
  publication-title: Science
– volume: 3
  start-page: 1716
  year: 2007
  end-page: 1726
  ident: br0240
  article-title: Signal propagation in proteins and relation to equilibrium fluctuations
  publication-title: PLoS Comput Biol
– volume: 2
  start-page: 173
  year: 1997
  end-page: 181
  ident: br0090
  article-title: Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
  publication-title: Fold Des
– volume: 79
  start-page: 2334
  year: 2011
  ident: br1850
  article-title: Validating and improving elastic network models with molecular dynamics simulations
  publication-title: Proteins
– volume: 5
  start-page: 823
  year: 1986
  end-page: 826
  ident: br0280
  article-title: The relation between the divergence of sequence and structure in proteins
  publication-title: EMBO J
– volume: 357
  start-page: 543
  year: 1992
  end-page: 544
  ident: br0260
  article-title: One thousand families for the molecular biologist
  publication-title: Nature
– volume: 7
  start-page: e33931
  year: 2012
  ident: br0560
  article-title: Exploring protein dynamics space: the dynasome as the missing link between protein structure and function
  publication-title: PLoS ONE
– volume: 104
  start-page: 228103
  year: 2010
  ident: br0950
  article-title: Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins
  publication-title: Phys Rev Lett
– volume: 56
  start-page: 143
  year: 2004
  end-page: 156
  ident: br1440
  article-title: A method for simultaneous alignment of multiple protein structures
  publication-title: Proteins
– volume: 25
  start-page: 1876
  year: 2009
  end-page: 1883
  ident: br1740
  article-title: Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to ob-fold domains
  publication-title: Bioinformatics
– volume: 33
  start-page: 496
  year: 1998
  end-page: 517
  ident: br0740
  article-title: Energy landscape of a native protein: jumping-among-minima model
  publication-title: Proteins
– volume: 3
  start-page: e121
  year: 2007
  ident: br1130
  article-title: Evolution of function in the “two dinucleotide binding domains” flavoproteins
  publication-title: PLoS Comput Biol
– volume: 25
  start-page: 2743
  year: 2009
  end-page: 2744
  ident: br0030
  article-title: PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
  publication-title: Bioinformatics
– volume: 87
  start-page: 088102
  year: 2001
  ident: br0970
  article-title: Conformations of proteins in equilibrium
  publication-title: Phys Rev Lett
– volume: 8
  start-page: e1002428
  year: 2012
  ident: br0500
  article-title: Collective dynamics differentiates functional divergence in protein evolution
  publication-title: PLoS Comput Biol
– volume: 104
  start-page: 796
  year: 2007
  end-page: 801
  ident: br1410
  article-title: A consensus view of protein dynamics
  publication-title: Proc Natl Acad Sci USA
– volume: 406
  start-page: 287
  year: 2000
  end-page: 290
  ident: br0930
  article-title: Optimal shapes of compact strings
  publication-title: Nature
– volume: 85
  start-page: 183
  year: 2011
  end-page: 215
  ident: br1150
  article-title: Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings
  publication-title: Adv Protein Chem Struct Biol
– volume: 131
  start-page: 6322
  year: 2009
  end-page: 6323
  ident: br0800
  article-title: Conservation of side-chain dynamics within a protein family
  publication-title: J Am Chem Soc
– volume: 63
  start-page: 448
  year: 2006
  end-page: 457
  ident: br0910
  article-title: Evolutionary conservation of protein backbone flexibility
  publication-title: J Mol Evol
– volume: 10
  start-page: 26
  year: 2010
  ident: br1750
  article-title: Comparing interfacial dynamics in protein–protein complexes: an elastic network approach
  publication-title: BMC Struct Biol
– volume: 13
  start-page: 565
  year: 2005
  end-page: 577
  ident: br1780
  article-title: Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved
  publication-title: Structure
– volume: 1
  start-page: 4
  year: 2010
  end-page: 8
  ident: br1620
  article-title: Mechanistic studies of Sansalvamide A-amide: an allosteric modulator of Hsp90
  publication-title: ACS Med Chem Lett
– volume: 15
  start-page: 565
  year: 2007
  end-page: 575
  ident: br1400
  article-title: Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
  publication-title: Structure
– volume: 320
  start-page: 1011
  year: 2002
  end-page: 1024
  ident: br0330
  article-title: Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model
  publication-title: J Mol Biol
– volume: 33
  start-page: 6739
  year: 1994
  end-page: 6749
  ident: br0490
  article-title: Structural mechanisms for domain movements in proteins
  publication-title: Biochemistry
– volume: 77
  start-page: 127148
  year: 2008
  ident: br1820
  article-title: Structure and mechanics of membrane proteins
  publication-title: Annu Rev Biochem
– volume: 271
  start-page: 618
  year: 1978
  end-page: 621
  ident: br1550
  article-title: Structural evidence for gene duplication in the evolution of the acid proteases
  publication-title: Nature
– volume: 55
  start-page: 635
  year: 2004
  end-page: 645
  ident: br0990
  article-title: Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models
  publication-title: Proteins
– volume: 3
  start-page: 936
  year: 1994
  end-page: 943
  ident: br0550
  article-title: Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis
  publication-title: Protein Sci
– volume: 13
  start-page: 1108
  year: 2004
  end-page: 1123
  ident: br1210
  article-title: HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
  publication-title: Protein Sci
– volume: 57
  start-page: 725
  year: 2004
  end-page: 733
  ident: br0770
  article-title: Automatic domain decomposition of proteins by a Gaussian network model
  publication-title: Proteins
– volume: 45
  start-page: 1173
  year: 2006
  end-page: 1182
  ident: br0780
  article-title: Loop motions of triosephosphate isomerase observed with elastic networks
  publication-title: Biochemistry
– volume: 19
  start-page: 881
  year: 2011
  end-page: 889
  ident: br1510
  article-title: A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks
  publication-title: Structure
– volume: 286
  start-page: 295
  year: 1999
  end-page: 299
  ident: br0860
  article-title: Evolutionarily conserved pathways of energetic connectivity in protein families
  publication-title: Science
– volume: 261
  start-page: 25
  year: 2000
  end-page: 37
  ident: br0630
  article-title: Harmonicity in slow protein dynamics
  publication-title: Chem Phys
– volume: 25
  start-page: 4876
  year: 1997
  end-page: 4882
  ident: br1570
  article-title: The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
  publication-title: Nucleic Acids Res
– volume: 89
  start-page: 14
  year: 2005
  end-page: 21
  ident: br0310
  article-title: Functional dynamics of PDZ binding domains: a normal-mode analysis
  publication-title: Biophys J
– volume: 295
  start-page: 1480
  year: 2002
  end-page: 1481
  ident: br0390
  article-title: Enzymology: a moving story
  publication-title: Science
– volume: 48
  start-page: 682
  year: 2002
  end-page: 695
  ident: br0760
  article-title: Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistics
  publication-title: Proteins
– volume: 6
  start-page: 2910
  year: 2010
  end-page: 2923
  ident: br0790
  article-title: Approaching elastic network models to atomistic molecular dynamics
  publication-title: J Chem Theor Comput
– volume: 9
  start-page: e1001193
  year: 2011
  ident: br1340
  article-title: Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis
  publication-title: PLoS Biol
– volume: 59
  start-page: 1007
  year: 1990
  end-page: 1039
  ident: br0270
  article-title: The classification and origins of protein folding patterns
  publication-title: Annu Rev Biochem
– volume: 29
  start-page: 2253
  year: 2012
  end-page: 2263
  ident: br0850
  article-title: Sequence evolution correlates with structural dynamics
  publication-title: Mol Biol Evol
– volume: 80
  start-page: 616625
  year: 2011
  ident: br1840
  article-title: Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
  publication-title: Proteins
– volume: 70
  start-page: 1235
  year: 2008
  end-page: 1242
  ident: br0620
  article-title: Solvent effects in the slow dynamics of proteins
  publication-title: Proteins
– volume: 100
  start-page: 6980
  year: 2003
  end-page: 6985
  ident: br1380
  article-title: Correlated motion and the effect of distal mutations in dihydrofolate reductase
  publication-title: Proc Natl Acad Sci USA
– volume: 105
  start-page: 4679
  year: 2008
  end-page: 4684
  ident: br0250
  article-title: Reassessing a sparse energetic network within a single protein domain
  publication-title: Proc Natl Acad Sci USA
– volume: 40
  start-page: 343
  year: 2012
  end-page: 350
  ident: br1370
  article-title: MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
  publication-title: Nucleic Acids Res
– volume: 98
  start-page: 048102
  year: 2007
  ident: br1240
  article-title: Anharmonicity and self-similarity of the free energy landscape of protein G
  publication-title: Phys Rev Lett
– volume: 25
  start-page: 2663
  year: 2009
  end-page: 2669
  ident: br1000
  article-title: Mistral: a tool for energy-based multiple structural alignment of proteins
  publication-title: Bioinformatics
– volume: 10
  start-page: 59
  year: 2003
  end-page: 69
  ident: br1520
  article-title: Evolutionarily conserved networks of residues mediate allosteric communication in proteins
  publication-title: Nat Struct Biol
– volume: 302
  start-page: 262
  year: 2003
  end-page: 266
  ident: br1690
  article-title: Protein conformational dynamics probed by single-molecule electron transfer
  publication-title: Science
– volume: 17
  start-page: 451
  year: 1988
  end-page: 479
  ident: br0440
  article-title: Conformational substates in proteins
  publication-title: Annu Rev Biophys Biophys Chem
– volume: 262
  start-page: 325
  year: 1976
  end-page: 326
  ident: br0940
  article-title: The hinge-bending mode in lysozyme
  publication-title: Nature
– volume: 275
  start-page: 73
  year: 1997
  end-page: 77
  ident: br1480
  article-title: Recognition of unique carboxyl-terminal motifs by distinct PDZ domains
  publication-title: Science
– volume: 80
  start-page: 1167
  year: 2012
  end-page: 1176
  ident: br1590
  article-title: Dynamics alignment: comparison of protein dynamics in the SCOP database
  publication-title: Proteins
– volume: 267
  start-page: 1619
  year: 1995
  end-page: 1620
  ident: br1670
  article-title: Navigating the folding routes
  publication-title: Science
– volume: 181
  start-page: 423
  year: 1985
  end-page: 447
  ident: br0830
  article-title: Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
  publication-title: J Mol Biol
– volume: 36
  start-page: 419
  year: 1999
  end-page: 424
  ident: br0050
  article-title: On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteinsʼ molecular dynamics simulations
  publication-title: Proteins
– volume: 7
  start-page: e1002193
  year: 2011
  ident: br1290
  article-title: Ligand-induced modulation of the free-energy landscape of g protein-coupled receptors explored by adaptive biasing techniques
  publication-title: PLoS Comput Biol
– volume: 1
  start-page: 790
  year: 2005
  end-page: 800
  ident: br1310
  article-title: Exploring the essential dynamics of b-B-DNA
  publication-title: J Chem Theory Comput
– volume: 14
  start-page: 633
  year: 2005
  end-page: 643
  ident: br0040
  article-title: Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool
  publication-title: Protein Sci
– volume: 109
  start-page: 1959
  year: 2005
  end-page: 1969
  ident: br1040
  article-title: Simple energy landscape model for the kinetics of functional transitions in proteins
  publication-title: J Phys Chem B
– volume: 17
  start-page: 918
  year: 2008
  end-page: 929
  ident: br1730
  article-title: Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families
  publication-title: Protein Sci
– volume: 111
  start-page: 12327
  year: 2007
  end-page: 12332
  ident: br0200
  article-title: Large-scale motions and electrostatic properties of furin and HIV-1 protease
  publication-title: J Phys Chem A
– volume: 19
  start-page: 158
  year: 2012
  end-page: 163
  ident: br0110
  article-title: Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating
  publication-title: Nat Struct Mol Biol
– volume: 422
  start-page: 7
  year: 2008
  end-page: 13
  ident: br0890
  article-title: Evolutionary conservation of protein vibrational dynamics
  publication-title: Gene
– volume: 106
  start-page: 21631
  year: 2009
  end-page: 21636
  ident: br0690
  article-title: Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
  publication-title: Proc Natl Acad Sci USA
– volume: 47
  start-page: 9227
  year: 2008
  end-page: 9233
  ident: br0140
  article-title: Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis
  publication-title: Biochemistry
– volume: 450
  start-page: 913
  year: 2007
  end-page: 916
  ident: br0580
  article-title: A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
  publication-title: Nature
– volume: 450
  start-page: 838
  year: 2007
  end-page: 844
  ident: br0590
  article-title: Intrinsic motions along an enzymatic reaction trajectory
  publication-title: Nature
– volume: 95
  start-page: 198103
  year: 2005
  ident: br1020
  article-title: Allostery in a coarse-grained model of protein dynamics
  publication-title: Phys Rev Lett
– volume: 25
  start-page: 1709
  year: 2009
  end-page: 1710
  ident: br0160
  article-title: FlexServ: an integrated tool for the analysis of protein flexibility
  publication-title: Bioinformatics
– volume: 332
  start-page: 234
  year: 2011
  end-page: 238
  ident: br0120
  article-title: A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
  publication-title: Science
– volume: 68
  start-page: 2696
  year: 1992
  end-page: 2699
  ident: br0470
  article-title: Large-amplitude nonlinear motions in proteins
  publication-title: Phys Rev Lett
– volume: 82
  start-page: 3372
  year: 1999
  end-page: 3375
  ident: br0980
  article-title: Protein structures and optimal folding from a geometrical variational principle
  publication-title: Phys Rev Lett
– volume: 67
  start-page: 350
  year: 2007
  end-page: 359
  ident: br1420
  article-title: Locating the active sites of enzymes using mechanical properties
  publication-title: Proteins
– volume: 26
  start-page: 1055
  year: 2009
  end-page: 1065
  ident: br1660
  article-title: The effect of sequence evolution on protein structural divergence
  publication-title: Mol Biol Evol
– volume: 128
  start-page: 9766
  year: 2006
  end-page: 9772
  ident: br0190
  article-title: Convergent dynamics in the protease enzymatic superfamily
  publication-title: J Am Chem Soc
– volume: 33
  start-page: 252
  year: 2005
  end-page: 255
  ident: br1300
  article-title: GenDiS: genomic distribution of protein structural domain superfamilies
  publication-title: Nucleic Acids Res
– volume: 65
  start-page: 031910
  year: 2002
  ident: br0600
  article-title: Convergence of sampling in protein simulations
  publication-title: Phys Rev E
– volume: 75
  start-page: 707712
  year: 2006
  ident: br1860
  article-title: Introduction to the membrane protein reviews: the interplay of structure, dynamics, and environment in membrane protein function
  publication-title: Annu Rev Biochem
– volume: 14
  start-page: 33
  year: 1996
  end-page: 38
  ident: br0680
  article-title: VMD – visual molecular dynamics
  publication-title: J Mol Graph
– volume: 91
  start-page: 2115
  year: 2006
  end-page: 2120
  ident: br0520
  article-title: A natural coarse graining for simulating large biomolecular motion
  publication-title: Biophys J
– volume: 88
  start-page: 1291
  year: 2005
  end-page: 1299
  ident: br0810
  article-title: An analysis of core deformations in protein superfamilies
  publication-title: Biophys J
– volume: 106
  start-page: 15690
  year: 2009
  end-page: 15695
  ident: br1450
  article-title: The continuity of protein structure space is an intrinsic property of proteins
  publication-title: Proc Natl Acad Sci USA
– volume: 89
  start-page: 3
  year: 2005
  end-page: 13
  ident: br0900
  article-title: Exploring the common dynamics of homologous proteins. Application to the globin family
  publication-title: Biophys J
– volume: 32
  start-page: 582
  year: 2004
  end-page: 585
  ident: br1700
  article-title: FATCAT: a web server for flexible structure comparison and structure similarity searching
  publication-title: Nucleic Acids Res
– volume: 32
  start-page: 203
  year: 2004
  end-page: 207
  ident: br1500
  article-title: HOMSTRAD: recent developments of the homologous protein structure alignment database
  publication-title: Nucleic Acids Res
– year: 2002
  ident: br0420
  article-title: Protein physics
– volume: 61
  start-page: 809
  year: 2005
  end-page: 822
  ident: br1170
  article-title: Comparative molecular dynamics—similar folds and similar motions?
  publication-title: Proteins
– volume: 59
  start-page: 105
  year: 2008
  end-page: 127
  ident: br1720
  article-title: Understanding protein evolution: from protein physics to Darwinian selection
  publication-title: Annu Rev Phys Chem
– volume: 74
  start-page: 145
  year: 2009
  end-page: 154
  ident: br0750
  article-title: Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
  publication-title: Proteins
– volume: 19
  start-page: 285206
  year: 2007
  ident: br0180
  article-title: Structural and dynamical alignment of enzymes with partial structural similarity
  publication-title: J Phys Condens Matter
– volume: 22
  start-page: 3600
  year: 1994
  end-page: 3609
  ident: br0660
  article-title: The FSSP database of structurally aligned protein fold families
  publication-title: Nucleic Acids Res
– volume: 84
  start-page: 1931
  year: 2012
  end-page: 1937
  ident: br0350
  article-title: Why are the low-energy protein normal modes evolutionarily conserved?
  publication-title: Pure Appl Chem
– volume: 80
  start-page: 3696
  year: 1983
  end-page: 3700
  ident: br0510
  article-title: Dynamics of a small globular protein in terms of low-frequency vibrational modes
  publication-title: Proc Natl Acad Sci USA
– volume: 16
  start-page: 1141
  year: 2009
  end-page: 1147
  ident: br1600
  article-title: Hsp90 charged-linker truncation reverses the functional consequences of weakened hydrophobic contacts in the n domain
  publication-title: Nat Struct Mol Biol
– volume: 48
  start-page: 443
  year: 1970
  end-page: 453
  ident: br1120
  article-title: A general method applicable to the search for similarities in the amino acid sequence of two proteins
  publication-title: J Mol Biol
– volume: 99
  start-page: 2794
  year: 2002
  end-page: 2799
  ident: br0010
  article-title: Network of coupled promoting motions in enzyme catalysis
  publication-title: Proc Natl Acad Sci USA
– volume: 105
  start-page: 973
  year: 2005
  end-page: 999
  ident: br1610
  article-title: Proteases universally recognize beta strands in their active sites
  publication-title: Chem Rev
– volume: 78
  start-page: 2093
  year: 2000
  end-page: 2106
  ident: br0730
  article-title: Proteins with similar architecture exhibit similar large-scale dynamic behavior
  publication-title: Biophys J
– volume: 104
  start-page: 11627
  year: 2007
  end-page: 11632
  ident: br0960
  article-title: The network of sequence flow between protein structures
  publication-title: Proc Natl Acad Sci USA
– volume: 6
  start-page: 453
  year: 2000
  end-page: 458
  ident: br1490
  article-title: Assessing the protease and protease inhibitor content of the human genome
  publication-title: J Pept Sci
– volume: 10
  start-page: 128
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1790
  article-title: Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks
  publication-title: Curr Protein Pept Sci
  doi: 10.2174/138920309787847608
– volume: 23
  start-page: 1099
  year: 1984
  ident: 10.1016/j.plrev.2012.10.009_br0840
  article-title: Quasi-harmonic method for studying very low frequency modes in proteins
  publication-title: Biopolymers
  doi: 10.1002/bip.360230610
– volume: 5
  start-page: e1000331
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1180
  article-title: Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1000331
– volume: 181
  start-page: 423
  year: 1985
  ident: 10.1016/j.plrev.2012.10.009_br0830
  article-title: Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
  publication-title: J Mol Biol
  doi: 10.1016/0022-2836(85)90230-X
– volume: 56
  start-page: 143
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br1440
  article-title: A method for simultaneous alignment of multiple protein structures
  publication-title: Proteins
  doi: 10.1002/prot.10628
– volume: 247
  start-page: 536
  year: 1995
  ident: 10.1016/j.plrev.2012.10.009_br1100
  article-title: SCOP: a structural classification of proteins database for the investigation of sequences and structures
  publication-title: J Mol Biol
  doi: 10.1016/S0022-2836(05)80134-2
– volume: 357
  start-page: 543
  year: 1992
  ident: 10.1016/j.plrev.2012.10.009_br0260
  article-title: One thousand families for the molecular biologist
  publication-title: Nature
  doi: 10.1038/357543a0
– volume: 80
  start-page: 1167
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br1590
  article-title: Dynamics alignment: comparison of protein dynamics in the SCOP database
  publication-title: Proteins
  doi: 10.1002/prot.24017
– volume: 15
  start-page: 385
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1430
  article-title: Protein structure and evolutionary history determine sequence space topology
  publication-title: Genome Res
  doi: 10.1101/gr.3133605
– volume: 33
  start-page: 417
  year: 1998
  ident: 10.1016/j.plrev.2012.10.009_br0610
  article-title: Analysis of domain motions by approximate normal mode calculations
  publication-title: Proteins
  doi: 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2-8
– volume: 3
  start-page: e121
  issue: 7
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1130
  article-title: Evolution of function in the “two dinucleotide binding domains” flavoproteins
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.0030121
– volume: 32
  start-page: 189
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br0230
  article-title: The astral compendium in 2004
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkh034
– volume: 100
  start-page: 12570
  year: 2003
  ident: 10.1016/j.plrev.2012.10.009_br1030
  article-title: Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.2135471100
– volume: 45
  start-page: 2545
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1200
  article-title: Leveraging enzyme structure–function relationships for functional inference and experimental design: the structure–function linkage database
  publication-title: Biochemistry
  doi: 10.1021/bi052101l
– volume: 10
  start-page: 146
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1640
  article-title: Intra and inter-molecular communications through protein structure network
  publication-title: Curr Protein Pept Sci
  doi: 10.2174/138920309787847590
– year: 1993
  ident: 10.1016/j.plrev.2012.10.009_br0290
– volume: 98
  start-page: 048102
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1240
  article-title: Anharmonicity and self-similarity of the free energy landscape of protein G
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.98.048102
– volume: 71
  start-page: 45
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1530
  article-title: Predicting the order in which contacts are broken during single molecule protein stretching experiments
  publication-title: Proteins
  doi: 10.1002/prot.21652
– volume: 94
  start-page: 198302
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1010
  article-title: Observation of a power-law memory kernel for fluctuations within a single protein molecule
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.94.198302
– volume: 66
  start-page: 2231
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1560
  article-title: Functional aspects of protein flexibility
  publication-title: Cell Mol Life Sci
  doi: 10.1007/s00018-009-0014-6
– volume: 19
  start-page: 158
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0110
  article-title: Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating
  publication-title: Nat Struct Mol Biol
  doi: 10.1038/nsmb.2208
– volume: 79
  start-page: 2334
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1850
  article-title: Validating and improving elastic network models with molecular dynamics simulations
  publication-title: Proteins
  doi: 10.1002/prot.22855
– volume: 1
  start-page: 4
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br1620
  article-title: Mechanistic studies of Sansalvamide A-amide: an allosteric modulator of Hsp90
  publication-title: ACS Med Chem Lett
  doi: 10.1021/ml900003t
– volume: 7
  start-page: e1002154
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1830
  article-title: Change in allosteric network affects binding affinities of PDZ domains: analysis through perturbation response scanning
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1002154
– volume: 96
  start-page: 4993
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1280
  article-title: Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits
  publication-title: Biophys J
  doi: 10.1016/j.bpj.2009.03.051
– volume: 105
  start-page: 4679
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br0250
  article-title: Reassessing a sparse energetic network within a single protein domain
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0711732105
– volume: 331
  start-page: 829
  year: 2003
  ident: 10.1016/j.plrev.2012.10.009_br0100
  article-title: Catalysing new reactions during evolution: economy of residues and mechanism
  publication-title: J Mol Biol
  doi: 10.1016/S0022-2836(03)00734-4
– volume: 27
  start-page: 425
  year: 1997
  ident: 10.1016/j.plrev.2012.10.009_br0540
  article-title: Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme
  publication-title: Proteins
  doi: 10.1002/(SICI)1097-0134(199703)27:3<425::AID-PROT10>3.0.CO;2-N
– volume: 273
  start-page: 595
  year: 1996
  ident: 10.1016/j.plrev.2012.10.009_br0670
  article-title: Mapping the protein universe
  publication-title: Science
  doi: 10.1126/science.273.5275.595
– year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0420
– volume: 8
  start-page: e1002749
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br1080
  article-title: The role of flexibility and conformational selection in the binding promiscuity of PDZ domains
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1002749
– volume: 17
  start-page: 918
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br1730
  article-title: Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families
  publication-title: Protein Sci
  doi: 10.1110/ps.073390208
– volume: 84
  start-page: 3009
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br0920
  article-title: Role of secondary motifs in fast folding polymers: a dynamical variational principle
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.84.3009
– volume: 95
  start-page: 198103
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1020
  article-title: Allostery in a coarse-grained model of protein dynamics
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.95.198103
– volume: 406
  start-page: 287
  issue: 6793
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br0930
  article-title: Optimal shapes of compact strings
  publication-title: Nature
  doi: 10.1038/35018538
– volume: 61
  start-page: 809
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1170
  article-title: Comparative molecular dynamics—similar folds and similar motions?
  publication-title: Proteins
  doi: 10.1002/prot.20672
– year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br0820
– volume: 63
  start-page: 448
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0910
  article-title: Evolutionary conservation of protein backbone flexibility
  publication-title: J Mol Evol
  doi: 10.1007/s00239-005-0209-x
– volume: 37
  start-page: 239
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1320
  article-title: The Degradome database: mammalian proteases and diseases of proteolysis
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkn570
– volume: 2
  start-page: 173
  year: 1997
  ident: 10.1016/j.plrev.2012.10.009_br0090
  article-title: Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential
  publication-title: Fold Des
  doi: 10.1016/S1359-0278(97)00024-2
– volume: 320
  start-page: 1011
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0330
  article-title: Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model
  publication-title: J Mol Biol
  doi: 10.1016/S0022-2836(02)00562-4
– volume: 16
  start-page: 1141
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1600
  article-title: Hsp90 charged-linker truncation reverses the functional consequences of weakened hydrophobic contacts in the n domain
  publication-title: Nat Struct Mol Biol
  doi: 10.1038/nsmb.1682
– volume: 33
  start-page: 6739
  year: 1994
  ident: 10.1016/j.plrev.2012.10.009_br0490
  article-title: Structural mechanisms for domain movements in proteins
  publication-title: Biochemistry
  doi: 10.1021/bi00188a001
– volume: 33
  start-page: 252
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1300
  article-title: GenDiS: genomic distribution of protein structural domain superfamilies
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gki087
– volume: 7
  start-page: e1002193
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1290
  article-title: Ligand-induced modulation of the free-energy landscape of g protein-coupled receptors explored by adaptive biasing techniques
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1002193
– volume: 422
  start-page: 7
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br0890
  article-title: Evolutionary conservation of protein vibrational dynamics
  publication-title: Gene
  doi: 10.1016/j.gene.2008.06.002
– volume: 33
  start-page: D247
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1190
  article-title: The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
  publication-title: Nucl Acids Res
  doi: 10.1093/nar/gki024
– volume: 87
  start-page: 088102
  year: 2001
  ident: 10.1016/j.plrev.2012.10.009_br0970
  article-title: Conformations of proteins in equilibrium
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.87.088102
– volume: 7
  start-page: 2469
  year: 1998
  ident: 10.1016/j.plrev.2012.10.009_br1050
  article-title: HOMSTRAD: a database of protein structure alignments for homologous families
  publication-title: Protein Sci
  doi: 10.1002/pro.5560071126
– volume: 17
  start-page: 451
  year: 1988
  ident: 10.1016/j.plrev.2012.10.009_br0440
  article-title: Conformational substates in proteins
  publication-title: Annu Rev Biophys Biophys Chem
  doi: 10.1146/annurev.bb.17.060188.002315
– volume: 1
  start-page: 790
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1310
  article-title: Exploring the essential dynamics of b-B-DNA
  publication-title: J Chem Theory Comput
  doi: 10.1021/ct050051s
– volume: 91
  start-page: 2115
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0520
  article-title: A natural coarse graining for simulating large biomolecular motion
  publication-title: Biophys J
  doi: 10.1529/biophysj.106.083568
– volume: 84
  start-page: 1931
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0350
  article-title: Why are the low-energy protein normal modes evolutionarily conserved?
  publication-title: Pure Appl Chem
  doi: 10.1351/PAC-CON-12-02-15
– volume: 32
  start-page: 582
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br1700
  article-title: FATCAT: a web server for flexible structure comparison and structure similarity searching
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkh430
– volume: 19
  start-page: 285206
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0180
  article-title: Structural and dynamical alignment of enzymes with partial structural similarity
  publication-title: J Phys Condens Matter
  doi: 10.1088/0953-8984/19/28/285206
– volume: 74
  start-page: 145
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0750
  article-title: Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis
  publication-title: Proteins
  doi: 10.1002/prot.22139
– volume: 105
  start-page: 5441
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br1680
  article-title: Detecting evolutionary relationships across existing fold space, using sequence order-independent profile–profile alignments
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0704422105
– volume: 82
  start-page: 3372
  year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0980
  article-title: Protein structures and optimal folding from a geometrical variational principle
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.82.3372
– volume: 63
  start-page: 197
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1470
  article-title: An enhanced elastic network model to represent the motions of domain-swapped proteins
  publication-title: Proteins
  doi: 10.1002/prot.20836
– volume: 80
  start-page: 616625
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1840
  article-title: Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
  publication-title: Proteins
– volume: 286
  start-page: 295
  year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0860
  article-title: Evolutionarily conserved pathways of energetic connectivity in protein families
  publication-title: Science
  doi: 10.1126/science.286.5438.295
– volume: 26
  start-page: 1055
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1660
  article-title: The effect of sequence evolution on protein structural divergence
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msp020
– volume: 6
  start-page: 4245
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0170
  article-title: Essential dynamics of helices provide a functional classification of EF-hand proteins
  publication-title: J Proteome Res
  doi: 10.1021/pr070314m
– volume: 450
  start-page: 838
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0590
  article-title: Intrinsic motions along an enzymatic reaction trajectory
  publication-title: Nature
  doi: 10.1038/nature06410
– volume: 105
  start-page: 973
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1610
  article-title: Proteases universally recognize beta strands in their active sites
  publication-title: Chem Rev
  doi: 10.1021/cr040669e
– volume: 80
  start-page: 505
  year: 2001
  ident: 10.1016/j.plrev.2012.10.009_br0080
  article-title: Anisotropy of fluctuation dynamics of proteins with an elastic network model
  publication-title: Biophys J
  doi: 10.1016/S0006-3495(01)76033-X
– volume: 131
  start-page: 6322
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0800
  article-title: Conservation of side-chain dynamics within a protein family
  publication-title: J Am Chem Soc
  doi: 10.1021/ja809915a
– volume: 57
  start-page: 725
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br0770
  article-title: Automatic domain decomposition of proteins by a Gaussian network model
  publication-title: Proteins
  doi: 10.1002/prot.20268
– volume: 13
  start-page: 565
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1780
  article-title: Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved
  publication-title: Structure
  doi: 10.1016/j.str.2005.01.017
– volume: 14
  start-page: 33
  year: 1996
  ident: 10.1016/j.plrev.2012.10.009_br0680
  article-title: VMD – visual molecular dynamics
  publication-title: J Mol Graph
  doi: 10.1016/0263-7855(96)00018-5
– volume: 275
  start-page: 73
  year: 1997
  ident: 10.1016/j.plrev.2012.10.009_br1480
  article-title: Recognition of unique carboxyl-terminal motifs by distinct PDZ domains
  publication-title: Science
  doi: 10.1126/science.275.5296.73
– volume: 48
  start-page: 682
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0760
  article-title: Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistics
  publication-title: Proteins
  doi: 10.1002/prot.10168
– volume: 11
  start-page: 188
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br1090
  article-title: Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
  publication-title: BMC Bioinform
  doi: 10.1186/1471-2105-11-188
– volume: 80
  start-page: 3696
  year: 1983
  ident: 10.1016/j.plrev.2012.10.009_br0510
  article-title: Dynamics of a small globular protein in terms of low-frequency vibrational modes
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.80.12.3696
– volume: 45
  start-page: 1173
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0780
  article-title: Loop motions of triosephosphate isomerase observed with elastic networks
  publication-title: Biochemistry
  doi: 10.1021/bi0518085
– volume: 17
  start-page: 412
  year: 1993
  ident: 10.1016/j.plrev.2012.10.009_br0060
  article-title: Essential dynamics of proteins
  publication-title: Proteins
  doi: 10.1002/prot.340170408
– volume: 104
  start-page: 228103
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br0950
  article-title: Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.104.228103
– volume: 319
  start-page: 567
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br1220
  article-title: Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease
  publication-title: J Mol Biol
  doi: 10.1016/S0022-2836(02)00301-7
– volume: 78
  start-page: 2093
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br0730
  article-title: Proteins with similar architecture exhibit similar large-scale dynamic behavior
  publication-title: Biophys J
  doi: 10.1016/S0006-3495(00)76756-7
– volume: 99
  start-page: 2794
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0010
  article-title: Network of coupled promoting motions in enzyme catalysis
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.052005999
– volume: 27
  start-page: 2843
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br0870
  article-title: iMod: multipurpose normal mode analysis in internal coordinates
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr497
– volume: 74
  start-page: 867
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1140
  article-title: Protein families and their evolution—a structural perspective
  publication-title: Annu Rev Biochem
  doi: 10.1146/annurev.biochem.74.082803.133029
– volume: 68
  start-page: 2696
  year: 1992
  ident: 10.1016/j.plrev.2012.10.009_br0470
  article-title: Large-amplitude nonlinear motions in proteins
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.68.2696
– volume: 75
  start-page: 707712
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1860
  article-title: Introduction to the membrane protein reviews: the interplay of structure, dynamics, and environment in membrane protein function
  publication-title: Annu Rev Biochem
  doi: 10.1146/annurev.biochem.75.110105.142336
– volume: 16
  start-page: 1522
  issue: 12
  year: 1995
  ident: 10.1016/j.plrev.2012.10.009_br0150
  article-title: Harmonic analysis of large systems I. Methodology
  publication-title: J Comput Chem
  doi: 10.1002/jcc.540161209
– volume: 9
  start-page: 6
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1630
  article-title: Comparison of molecular dynamics and superfamily spaces of protein domain deformation
  publication-title: BMC Struct Biol
  doi: 10.1186/1472-6807-9-6
– volume: 93
  start-page: 14243
  year: 1996
  ident: 10.1016/j.plrev.2012.10.009_br0130
  article-title: Symmetry, stability, and dynamics of multidomain and multicomponent protein systems
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.93.25.14243
– volume: 6
  start-page: 2910
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br0790
  article-title: Approaching elastic network models to atomistic molecular dynamics
  publication-title: J Chem Theor Comput
  doi: 10.1021/ct100208e
– volume: 119
  start-page: 84
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1710
  article-title: Hierarchical clustering of correlation patterns: new method of domain identification in proteins
  publication-title: Biophys Chem
  doi: 10.1016/j.bpc.2005.07.004
– volume: 11
  start-page: 2393
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br1230
  article-title: Drug resistance in HIV-1 protease: flexibility-assisted mechanism of compensatory mutations
  publication-title: Protein Sci
  doi: 10.1110/ps.0206702
– volume: 67
  start-page: 350
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1420
  article-title: Locating the active sites of enzymes using mechanical properties
  publication-title: Proteins
  doi: 10.1002/prot.21353
– volume: 59
  start-page: 105
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br1720
  article-title: Understanding protein evolution: from protein physics to Darwinian selection
  publication-title: Annu Rev Phys Chem
  doi: 10.1146/annurev.physchem.58.032806.104449
– volume: 262
  start-page: 325
  year: 1976
  ident: 10.1016/j.plrev.2012.10.009_br0940
  article-title: The hinge-bending mode in lysozyme
  publication-title: Nature
  doi: 10.1038/262325a0
– volume: 48
  start-page: 443
  year: 1970
  ident: 10.1016/j.plrev.2012.10.009_br1120
  article-title: A general method applicable to the search for similarities in the amino acid sequence of two proteins
  publication-title: J Mol Biol
  doi: 10.1016/0022-2836(70)90057-4
– volume: 29
  start-page: 2253
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0850
  article-title: Sequence evolution correlates with structural dynamics
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/mss097
– volume: 11
  start-page: 2606
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br1160
  article-title: Mammoth (matching molecular models obtained from theory): an automated method for model comparison
  publication-title: Protein Sci
  doi: 10.1110/ps.0215902
– volume: 77
  start-page: 1905
  year: 1996
  ident: 10.1016/j.plrev.2012.10.009_br1580
  article-title: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.77.1905
– volume: 106
  start-page: 21631
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0690
  article-title: Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0907548106
– volume: 89
  start-page: 3
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0900
  article-title: Exploring the common dynamics of homologous proteins. Application to the globin family
  publication-title: Biophys J
  doi: 10.1529/biophysj.104.053041
– volume: 47
  start-page: 9227
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br0140
  article-title: Conformational relaxation following hydride transfer plays a limiting role in dihydrofolate reductase catalysis
  publication-title: Biochemistry
  doi: 10.1021/bi801102e
– volume: 7
  start-page: e33931
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0560
  article-title: Exploring protein dynamics space: the dynasome as the missing link between protein structure and function
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0033931
– volume: 123
  start-page: 3499
  year: 2001
  ident: 10.1016/j.plrev.2012.10.009_br1330
  article-title: Neighboring side chain effects on asparaginyl and aspartyl degradation: an ab initio study of the relationship between peptide conformation and backbone NH acidity
  publication-title: J Am Chem Soc
  doi: 10.1021/ja0026814
– volume: 302
  start-page: 262
  year: 2003
  ident: 10.1016/j.plrev.2012.10.009_br1690
  article-title: Protein conformational dynamics probed by single-molecule electron transfer
  publication-title: Science
  doi: 10.1126/science.1086911
– volume: 13
  start-page: 1108
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br1210
  article-title: HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs
  publication-title: Protein Sci
  doi: 10.1110/ps.03468904
– volume: 38
  start-page: 41
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br1270
  article-title: Aladyn: a web server for aligning proteins by matching their large-scale motion
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkq293
– volume: 347
  start-page: 1077
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1460
  article-title: The relationship between the flexibility of proteins and their conformational states on forming protein–protein complexes with an application to protein–protein docking
  publication-title: J Mol Biol
  doi: 10.1016/j.jmb.2005.01.058
– volume: 93
  start-page: 2289
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1770
  article-title: Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations
  publication-title: Biophys J
  doi: 10.1529/biophysj.107.105270
– volume: 295
  start-page: 1480
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0390
  article-title: Enzymology: a moving story
  publication-title: Science
  doi: 10.1126/science.1069823
– volume: 63
  start-page: 513
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1360
  article-title: Protein superfamily evolution and the last universal common ancestor (LUCA)
  publication-title: J Mol Evol
  doi: 10.1007/s00239-005-0289-7
– volume: 79
  start-page: 2902
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br1800
  article-title: Protein motions at zero-total angular momentum: the importance of long-range correlations
  publication-title: Biophys J
  doi: 10.1016/S0006-3495(00)76527-1
– volume: 85
  start-page: 183
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1150
  article-title: Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings
  publication-title: Adv Protein Chem Struct Biol
  doi: 10.1016/B978-0-12-386485-7.00005-3
– volume: 111
  start-page: 12327
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0200
  article-title: Large-scale motions and electrostatic properties of furin and HIV-1 protease
  publication-title: J Phys Chem A
  doi: 10.1021/jp0751716
– volume: 32
  start-page: 203
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br1500
  article-title: HOMSTRAD: recent developments of the homologous protein structure alignment database
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkh027
– volume: 14
  start-page: 1
  year: 2001
  ident: 10.1016/j.plrev.2012.10.009_br1540
  article-title: Conformational change of proteins arising from normal mode calculations
  publication-title: Protein Eng
  doi: 10.1093/protein/14.1.1
– volume: 16
  start-page: 566
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br0650
  article-title: Dalilite workbench for protein structure comparison
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/16.6.566
– volume: 106
  start-page: 15690
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1450
  article-title: The continuity of protein structure space is an intrinsic property of proteins
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0907683106
– volume: 361
  start-page: 441
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0430
  article-title: The proteome: structure, function and evolution
  publication-title: Philos Trans R Soc Lond B Biol Sci
  doi: 10.1098/rstb.2005.1802
– volume: 450
  start-page: 913
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0580
  article-title: A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
  publication-title: Nature
  doi: 10.1038/nature06407
– volume: 312
  start-page: 111
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1650
  article-title: Darwinian evolution can follow only very few mutational paths to fitter proteins
  publication-title: Science
  doi: 10.1126/science.1123539
– volume: 88
  start-page: 1291
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0810
  article-title: An analysis of core deformations in protein superfamilies
  publication-title: Biophys J
  doi: 10.1529/biophysj.104.052449
– year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0410
– volume: 77
  start-page: 127148
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br1820
  article-title: Structure and mechanics of membrane proteins
  publication-title: Annu Rev Biochem
  doi: 10.1146/annurev.biochem.77.062706.154450
– volume: 6
  start-page: e15827
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1350
  article-title: Discovering conformational sub-states relevant to protein function
  publication-title: PLoS ONE
  doi: 10.1371/journal.pone.0015827
– volume: 15
  start-page: 565
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1400
  article-title: Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
  publication-title: Structure
  doi: 10.1016/j.str.2007.03.013
– volume: 78
  start-page: 173
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br0360
  article-title: A perturbative view of protein structural variation
  publication-title: Proteins
  doi: 10.1002/prot.22553
– volume: 19
  start-page: 881
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1510
  article-title: A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks
  publication-title: Structure
  doi: 10.1016/j.str.2011.03.009
– volume: 8
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br1060
  article-title: Corresponding functional dynamics across the Hsp90 chaperone family: insights from a multiscale analysis of MD simulations
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1002433
– volume: 332
  start-page: 234
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br0120
  article-title: A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis
  publication-title: Science
  doi: 10.1126/science.1198542
– volume: 25
  start-page: 4876
  year: 1997
  ident: 10.1016/j.plrev.2012.10.009_br1570
  article-title: The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/25.24.4876
– volume: 89
  start-page: 14
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0310
  article-title: Functional dynamics of PDZ binding domains: a normal-mode analysis
  publication-title: Biophys J
  doi: 10.1529/biophysj.104.055004
– volume: 16
  start-page: 1544
  issue: 12
  year: 1995
  ident: 10.1016/j.plrev.2012.10.009_br0710
  article-title: Harmonic analysis of large systems III. Comparison with molecular dynamics
  publication-title: J Comput Chem
– volume: 254
  start-page: 1598
  year: 1991
  ident: 10.1016/j.plrev.2012.10.009_br0450
  article-title: The energy landscapes and motions of proteins
  publication-title: Science
  doi: 10.1126/science.1749933
– volume: 75
  start-page: 519
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0530
  article-title: Relating protein motion to catalysis
  publication-title: Annu Rev Biochem
  doi: 10.1146/annurev.biochem.75.103004.142800
– volume: 103
  start-page: 767
  year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0400
  article-title: PDZ domains: fundamental building blocks in the organization of protein complexes at the plasma membrane
  publication-title: J Clin Invest
  doi: 10.1172/JCI6509
– volume: 34
  start-page: 369
  year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0640
  article-title: Analysis of domain motion in large proteins
  publication-title: Proteins
  doi: 10.1002/(SICI)1097-0134(19990215)34:3<369::AID-PROT9>3.0.CO;2-F
– volume: 127
  start-page: 3734
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0210
  article-title: Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
  publication-title: J Am Chem Soc
  doi: 10.1021/ja044608+
– volume: 65
  start-page: 031910
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0600
  article-title: Convergence of sampling in protein simulations
  publication-title: Phys Rev E
  doi: 10.1103/PhysRevE.65.031910
– volume: 132
  start-page: 6366
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br0300
  article-title: X-ray snapshot of HIV-1 protease in action: observation of tetrahedral intermediate and short ionic hydrogen bond SIHB with catalytic aspartate
  publication-title: J Am Chem Soc
  doi: 10.1021/ja100002b
– volume: 22
  start-page: 3600
  year: 1994
  ident: 10.1016/j.plrev.2012.10.009_br0660
  article-title: The FSSP database of structurally aligned protein fold families
  publication-title: Nucleic Acids Res
– volume: 25
  start-page: 2663
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1000
  article-title: Mistral: a tool for energy-based multiple structural alignment of proteins
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp506
– year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0460
  article-title: Measuring and comparing structural fluctuation patterns in large protein datasets
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts445
– volume: 3
  start-page: 1716
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0240
  article-title: Signal propagation in proteins and relation to equilibrium fluctuations
  publication-title: PLoS Comput Biol
– volume: 70
  start-page: 1235
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br0620
  article-title: Solvent effects in the slow dynamics of proteins
  publication-title: Proteins
  doi: 10.1002/prot.21655
– volume: 103
  start-page: 2605
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br1760
  article-title: On the origin and highly likely completeness of single-domain protein structures
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0509379103
– volume: 450
  start-page: 964
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0570
  article-title: Dynamic personalities of proteins
  publication-title: Nature
  doi: 10.1038/nature06522
– volume: 5
  start-page: e1000323
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1070
  article-title: Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1000323
– volume: 95
  start-page: 5901
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br1250
  article-title: Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics
  publication-title: Biophys J
  doi: 10.1529/biophysj.108.135467
– volume: 9
  start-page: e1001193
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1340
  article-title: Evolutionarily conserved linkage between enzyme fold, flexibility, and catalysis
  publication-title: PLoS Biol
  doi: 10.1371/journal.pbio.1001193
– volume: 6
  start-page: 453
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br1490
  article-title: Assessing the protease and protease inhibitor content of the human genome
  publication-title: J Pept Sci
  doi: 10.1002/1099-1387(200009)6:9<453::AID-PSC284>3.0.CO;2-Z
– volume: 17
  start-page: 1042
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0320
  article-title: The origin of allosteric functional modulation: multiple pre-existing pathways
  publication-title: Structure
  doi: 10.1016/j.str.2009.06.008
– volume: 49
  start-page: 9078
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br0720
  article-title: The tail wagging the dog: insights into catalysis in R67 dihydrofolate reductase
  publication-title: Biochemistry
  doi: 10.1021/bi1007222
– volume: 14
  start-page: 644
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br1110
  article-title: Coupled motions in enzyme catalysis
  publication-title: Curr Opin Chem Biol
  doi: 10.1016/j.cbpa.2010.07.020
– volume: 27
  start-page: 1575
  year: 2011
  ident: 10.1016/j.plrev.2012.10.009_br1810
  article-title: Prody: protein dynamics inferred from theory and experiments
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr168
– volume: 128
  start-page: 9766
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0190
  article-title: Convergent dynamics in the protease enzymatic superfamily
  publication-title: J Am Chem Soc
  doi: 10.1021/ja060896t
– volume: 2
  start-page: 464
  issue: 3
  year: 2006
  ident: 10.1016/j.plrev.2012.10.009_br0880
  article-title: A new method for coarse-grained elastic normal-mode analysis
  publication-title: J Chem Theory Comput
  doi: 10.1021/ct050307u
– volume: 271
  start-page: 618
  year: 1978
  ident: 10.1016/j.plrev.2012.10.009_br1550
  article-title: Structural evidence for gene duplication in the evolution of the acid proteases
  publication-title: Nature
  doi: 10.1038/271618a0
– volume: 438
  start-page: 117
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0380
  article-title: Intrinsic dynamics of an enzyme underlies catalysis
  publication-title: Nature
  doi: 10.1038/nature04105
– volume: 32
  start-page: D129
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br1260
  article-title: The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data
  publication-title: Nucl Acids Res
  doi: 10.1093/nar/gkh028
– volume: 33
  start-page: 496
  year: 1998
  ident: 10.1016/j.plrev.2012.10.009_br0740
  article-title: Energy landscape of a native protein: jumping-among-minima model
  publication-title: Proteins
  doi: 10.1002/(SICI)1097-0134(19981201)33:4<496::AID-PROT4>3.0.CO;2-1
– volume: 55
  start-page: 635
  year: 2004
  ident: 10.1016/j.plrev.2012.10.009_br0990
  article-title: Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models
  publication-title: Proteins
  doi: 10.1002/prot.20049
– volume: 36
  start-page: 419
  year: 2008
  ident: 10.1016/j.plrev.2012.10.009_br0070
  article-title: Data growth and its impact on the SCOP database: new developments
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkm993
– volume: 25
  start-page: 1709
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0160
  article-title: FlexServ: an integrated tool for the analysis of protein flexibility
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp304
– volume: 3
  start-page: 936
  year: 1994
  ident: 10.1016/j.plrev.2012.10.009_br0550
  article-title: Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis
  publication-title: Protein Sci
  doi: 10.1002/pro.5560030608
– volume: 25
  start-page: 2743
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br0030
  article-title: PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp512
– volume: 14
  start-page: 633
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0040
  article-title: Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool
  publication-title: Protein Sci
  doi: 10.1110/ps.04882105
– volume: 109
  start-page: 1959
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br1040
  article-title: Simple energy landscape model for the kinetics of functional transitions in proteins
  publication-title: J Phys Chem B
  doi: 10.1021/jp046736q
– volume: 10
  start-page: 59
  year: 2003
  ident: 10.1016/j.plrev.2012.10.009_br1520
  article-title: Evolutionarily conserved networks of residues mediate allosteric communication in proteins
  publication-title: Nat Struct Biol
  doi: 10.1038/nsb881
– volume: 104
  start-page: 11627
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br0960
  article-title: The network of sequence flow between protein structures
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0701393104
– volume: 100
  start-page: 6980
  year: 2003
  ident: 10.1016/j.plrev.2012.10.009_br1380
  article-title: Correlated motion and the effect of distal mutations in dihydrofolate reductase
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.1230801100
– volume: 104
  start-page: 796
  year: 2007
  ident: 10.1016/j.plrev.2012.10.009_br1410
  article-title: A consensus view of protein dynamics
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.0605534104
– volume: 10
  start-page: 26
  year: 2010
  ident: 10.1016/j.plrev.2012.10.009_br1750
  article-title: Comparing interfacial dynamics in protein–protein complexes: an elastic network approach
  publication-title: BMC Struct Biol
  doi: 10.1186/1472-6807-10-26
– volume: 25
  start-page: 1876
  year: 2009
  ident: 10.1016/j.plrev.2012.10.009_br1740
  article-title: Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to ob-fold domains
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp339
– volume: 59
  start-page: 1007
  year: 1990
  ident: 10.1016/j.plrev.2012.10.009_br0270
  article-title: The classification and origins of protein folding patterns
  publication-title: Annu Rev Biochem
  doi: 10.1146/annurev.bi.59.070190.005043
– volume: 8
  start-page: e1002428
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br0500
  article-title: Collective dynamics differentiates functional divergence in protein evolution
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1002428
– volume: 6
  start-page: 678
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0340
  article-title: Missense meanderings in sequence space: a biophysical view of protein evolution
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg1672
– volume: 267
  start-page: 1619
  year: 1995
  ident: 10.1016/j.plrev.2012.10.009_br1670
  article-title: Navigating the folding routes
  publication-title: Science
  doi: 10.1126/science.7886447
– volume: 26
  start-page: 4280
  year: 1998
  ident: 10.1016/j.plrev.2012.10.009_br0480
  article-title: A database of macromolecular motions
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/26.18.4280
– volume: 261
  start-page: 25
  year: 2000
  ident: 10.1016/j.plrev.2012.10.009_br0630
  article-title: Harmonicity in slow protein dynamics
  publication-title: Chem Phys
  doi: 10.1016/S0301-0104(00)00222-6
– volume: 40
  start-page: 343
  year: 2012
  ident: 10.1016/j.plrev.2012.10.009_br1370
  article-title: MEROPS: the database of proteolytic enzymes, their substrates and inhibitors
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkr987
– volume: 36
  start-page: 419
  year: 1999
  ident: 10.1016/j.plrev.2012.10.009_br0050
  article-title: On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteinsʼ molecular dynamics simulations
  publication-title: Proteins
  doi: 10.1002/(SICI)1097-0134(19990901)36:4<419::AID-PROT5>3.0.CO;2-U
– volume: 5
  start-page: 823
  year: 1986
  ident: 10.1016/j.plrev.2012.10.009_br0280
  article-title: The relation between the divergence of sequence and structure in proteins
  publication-title: EMBO J
  doi: 10.1002/j.1460-2075.1986.tb04288.x
– volume: 127
  start-page: 3734
  year: 2005
  ident: 10.1016/j.plrev.2012.10.009_br0220
  article-title: Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
  publication-title: J Am Chem Soc
  doi: 10.1021/ja044608+
– volume: 295
  start-page: 1520
  year: 2002
  ident: 10.1016/j.plrev.2012.10.009_br0370
  article-title: Enzyme dynamics during catalysis
  publication-title: Science
  doi: 10.1126/science.1066176
– volume: 16
  start-page: 1543
  issue: 12
  year: 1995
  ident: 10.1016/j.plrev.2012.10.009_br0700
  article-title: Harmonic analysis of large systems ii. comparison of different protein models
  publication-title: J Comput Chem
  doi: 10.1002/jcc.540161210
– reference: 23157841 - Phys Life Rev. 2013 Mar;10(1):35-6; discussion 39-40
– reference: 23154221 - Phys Life Rev. 2013 Mar;10(1):29-30; discussion 39-40
– reference: 23141839 - Phys Life Rev. 2013 Mar;10(1):31-2; discussion 39-40
– reference: 23154220 - Phys Life Rev. 2013 Mar;10(1):33-4; discussion 39-40
– reference: 23394959 - Phys Life Rev. 2013 Mar;10(1):37-8; discussion 39-40
– reference: 23122425 - Phys Life Rev. 2013 Mar;10(1):27-8; discussion 39-40
SSID ssj0032480
Score 2.2603722
SecondaryResourceType review_article
Snippet The growing interest for comparing protein internal dynamics owes much to the realisation that protein function can be accompanied or assisted by structural...
SourceID proquest
pubmed
crossref
elsevier
SourceType Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 1
SubjectTerms Animals
Databases, Protein
Humans
Molecular Dynamics Simulation
PDZ Domains
Peptide Hydrolases - chemistry
Peptide Hydrolases - metabolism
Proteins - chemistry
Proteins - metabolism
Structural Homology, Protein
Structure-Activity Relationship
Title Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments
URI https://dx.doi.org/10.1016/j.plrev.2012.10.009
https://www.ncbi.nlm.nih.gov/pubmed/23199577
https://www.proquest.com/docview/1328229076
Volume 10
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3JTsMwELUQCIkLYqcslZE4EtqkzmJuVUVVqOiBRXCLYseGIBSqLodegH_gD_kSZuwkEof2wCmSZTuWx_E8x2_eEHLqBqESKRxymkmSwAHFSN5q6WiWwMPnymticPLNIOg9sOsn_2mJdMpYGKRVFnu_3dPNbl2UNIrZbAyzrHHn-uAdAwYey1wYYEQ5YyGu8vOPiuYBeMFkT8PKDtYulYcMx2uImp_I7_LODcWLz_NO89Cn8ULdDbJewEfatiPcJEsq3yKrNqHkbJt8dmxawfyZGgGGLB9TMaPmNoBm9uffG01tFvrxBa0YeNTqyE5H6ufrG30d2ouOSqbcSzaEjkywC8UQpExWDaA_gPLPNlRuhzx0L-87PadIseDIls8njtZSs1YkFbilhEdMcKUDxRmHuXCThMHpw4MzhI6agBMBSbqSRzwQKPoOwFI2W7tkOX_P1T6h0I-MlPSYTlPGhC-4cHUomJdKLwy1qhGvnNpYFvrjmAbjLS6JZq-xsUeM9sBCGEONnFWNhlZ-Y3H1oLRZ_GcVxeAgFjc8KS0cw_eFlyZJrt6n4xhWltHED4Ma2bOmr0YC2JhzPwwP_vvaQ7LmmfQayGk7IstgOXUMIGci6mYV18lK-6rfG-Czf_vY_wWUogGh
linkProvider Elsevier
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV27TsMwFL0qRQgWxJvyNBIjoU3qPMyGKqoChQWQ2KzYsUsQChWFgQX4B_6QL-HaTiIxwMAUybIdy9fxPY7PPRdg349iJTI85HTSNMUDipW81dLTNMVHyFTQMcHJF5fR4Iae3Ya3DehVsTCGVlnu_W5Pt7t1WdIuZ7M9zvP2lR-id4woeix7YRBPwTTFz9ekMTh8q3keCBhs-jRT2zPVK-khS_IaG9FPQ_AKDi3Hi_3mnn6Dn9YN9RdgvsSP5NgNcREaqliCGZdR8nUZ3nsur2AxIlaBIS8mRLwSex1Acvf374FkLg395IjUFDzihGRfntTXx6dxdsZg5Kmiyt3lY-zIRrsQE4OUy7oB9odYfuRi5Vbgpn9y3Rt4ZY4FT3ZD9uxpLTXtJlKhX0pZQgVTOlKMMpwLP00pHj8CPETopINAEaGkL1nCImFU3xFZyk53FZrFY6HWgWA_MlEyoDrLKBWhYMLXsaBBJoM41qoFQTW1XJYC5CYPxgOvmGb33NqDG3uYQhxDCw7qRmOnv_F39aiyGf-xjDh6iL8b7lUW5viBmVuTtFCPLxOOS8uK4sdRC9ac6euRIDhmLIzjjf--dhdmB9cXQz48vTzfhLnA5towBLctaKIV1TYinmexY1f0N1eLAYw
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Comparing+proteins+by+their+internal+dynamics%3A+Exploring+structure%E2%80%93function+relationships+beyond+static+structural+alignments&rft.jtitle=Physics+of+life+reviews&rft.au=Micheletti%2C+Cristian&rft.date=2013-03-01&rft.pub=Elsevier+B.V&rft.issn=1571-0645&rft.eissn=1873-1457&rft.volume=10&rft.issue=1&rft.spage=1&rft.epage=26&rft_id=info:doi/10.1016%2Fj.plrev.2012.10.009&rft.externalDocID=S1571064512001327
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1571-0645&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1571-0645&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1571-0645&client=summon