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The location of the docking interface is determined largely by geometric complementarity, but finding complementary geometry is complicated by the flexibility of the backbone and side-chains of both proteins. We seek to generate candidates for docking that approximate the bound state well, even in cases where there is backbone and\/or side-chain difference from unbound to bound states.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We divide the surfaces of each protein into local patches and describe the effect of side-chain flexibility on each patch by sampling the space of conformations of its side-chains. Likely positions of individual side-chains are given by a rotamer library; this library is used to derive a sample of possible mutual conformations within the patch. We enforce broad coverage of torsion space. We control the size of the sample by using energy criteria to eliminate unlikely configurations, and by clustering similar configurations, resulting in 50 candidates for a patch, a manageable number for docking.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Using a database of protein dimers for which the bound and unbound structures of the monomers are known, we show that from the unbound patch we are able to generate candidates for docking that approximate the bound structure. In patches where backbone change is small (within 1 \u00c5 RMSD of bound), we are able to account for flexibility and generate candidates that are good approximations of the bound state (82% are within 1 \u00c5 and 98% are within 1.4 \u00c5 RMSD of the bound conformation). We also find that even in cases of moderate backbone flexibility our candidates are able to capture some of the overall shape change. Overall, in 650 of 700 test patches we produce a candidate that is either within 1 \u00c5 RMSD of the bound conformation or is closer to the bound state than the unbound is.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-575","type":"journal-article","created":{"date-parts":[[2010,11,24]],"date-time":"2010-11-24T07:13:57Z","timestamp":1290582837000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Sampling the conformation of protein surface residues for flexible protein docking"],"prefix":"10.1186","volume":"11","author":[{"given":"Patricia","family":"Francis-Lyon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengyin","family":"Gu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joel","family":"Hass","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nina","family":"Amenta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patrice","family":"Koehl","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,11,23]]},"reference":[{"key":"4158_CR1","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1016\/j.sbi.2006.02.002","volume":"16","author":"AM Bonvin","year":"2006","unstructured":"Bonvin AM: Flexible protein-protein docking. 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