PIE-Efficient filters and coarse grained potentials for unbound protein-protein docking
Identifying correct binding modes in a large set of models is an important step in protein–protein docking. We identified protein docking filter based on overlap area that significantly reduces the number of candidate structures that require detailed examination. We also developed potentials based o...
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Published in | Proteins, structure, function, and bioinformatics Vol. 78; no. 2; pp. 400 - 419 |
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Main Authors | , |
Format | Journal Article |
Language | English |
Published |
Hoboken
Wiley Subscription Services, Inc., A Wiley Company
01.02.2010
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Subjects | |
Online Access | Get full text |
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Summary: | Identifying correct binding modes in a large set of models is an important step in protein–protein docking. We identified protein docking filter based on overlap area that significantly reduces the number of candidate structures that require detailed examination. We also developed potentials based on residue contacts and overlap areas using a comprehensive learning set of 640 two‐chain protein complexes with mathematical programming. Our potential showed substantially better recognition capacity compared to other publicly accessible protein docking potentials in discriminating between native and nonnative binding modes on a large test set of 84 complexes independent of our training set. We were able to rank a near‐native model on the top in 43 cases and within top 10 in 51 cases. We also report an atomic potential that ranks a near‐native model on the top in 46 cases and within top 10 in 58 cases. Our filter+potential is well suited for selecting a small set of models to be refined to atomic resolution. Proteins 2010. © 2009 Wiley‐Liss, Inc. |
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Bibliography: | National Institutes of Health - No. GM067823 ark:/67375/WNG-Q4Z8TZMN-T ArticleID:PROT22550 istex:AB7218B55A057FC824B4CF1132DC6CB7D721FEC9 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ISSN: | 0887-3585 1097-0134 |
DOI: | 10.1002/prot.22550 |