{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T04:09:44Z","timestamp":1772165384165,"version":"3.50.1"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 \"\n                      <jats:italic>Decoys 'R' Us<\/jats:italic>\n                      \" decoy sets and in 24 out of 27 high-resolution CASP7\/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 \u00c5 for all residues and 0.73 \u00c5 for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/bioinfo.weizmann.ac.il\/hunter\/\" ext-link-type=\"uri\">http:\/\/bioinfo.weizmann.ac.il\/hunter\/<\/jats:ext-link>\n                      was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/1471-2105-11-374","type":"journal-article","created":{"date-parts":[[2010,7,30]],"date-time":"2010-07-30T15:00:29Z","timestamp":1280502029000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions"],"prefix":"10.1186","volume":"11","author":[{"given":"Vladimir","family":"Potapov","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mati","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuval","family":"Inbar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gideon","family":"Schreiber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,7,12]]},"reference":[{"key":"3831_CR1","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/S0959-440X(00)00063-4","volume":"10","author":"T Lazaridis","year":"2000","unstructured":"Lazaridis T, Karplus M: Effective energy functions for protein structure prediction. 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