Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins
We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters...
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Published in | Nucleic acids research Vol. 34; no. 21; pp. 6195 - 6204 |
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Main Authors | , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
Oxford Publishing Limited (England)
01.12.2006
Oxford University Press |
Subjects | |
Online Access | Get full text |
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Summary: | We describe here an energy based computer software suite for narrowing down the search space of tertiary structures of small globular proteins. The protocol comprises eight different computational modules that form an automated pipeline. It combines physics based potentials with biophysical filters to arrive at 10 plausible candidate structures starting from sequence and secondary structure information. The methodology has been validated here on 50 small globular proteins consisting of 2-3 helices and strands with known tertiary structures. For each of these proteins, a structure within 3-6 Å RMSD (root mean square deviation) of the native has been obtained in the 10 lowest energy structures. The protocol has been web enabled and is accessible at http://www.scfbio-iitd.res.in/bhageerath. |
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Bibliography: | http://www.nar.oupjournals.org/ ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Article-2 ObjectType-Feature-1 |
ISSN: | 0305-1048 1362-4962 |
DOI: | 10.1093/nar/gkl789 |