{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T15:15:44Z","timestamp":1722784544814},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,14]],"date-time":"2019-01-14T00:00:00Z","timestamp":1547424000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish grant","award":["BFU2016-76220-P"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Knowledge-based statistical potentials constitute a simpler and easier alternative to physics-based potentials in many applications, including folding, docking and protein modeling. Here, to improve the effectiveness of the current approximations, we attempt to capture the six-dimensional nature of residue\u2013residue interactions from known protein structures using a simple backbone-based representation.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We have developed KORP, a knowledge-based pairwise potential for proteins that depends on the relative position and orientation between residues. Using a minimalist representation of only three backbone atoms per residue, KORP utilizes a six-dimensional joint probability distribution to outperform state-of-the-art statistical potentials for native structure recognition and best model selection in recent critical assessment of protein structure prediction and loop-modeling benchmarks. Compared with the existing methods, our side-chain independent potential has a lower complexity and better efficiency. The superior accuracy and robustness of KORP represent a promising advance for protein modeling and refinement applications that require a fast but highly discriminative energy function.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n http:\/\/chaconlab.org\/modeling\/korp.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz026","type":"journal-article","created":{"date-parts":[[2019,1,9]],"date-time":"2019-01-09T04:12:16Z","timestamp":1547007136000},"page":"3013-3019","source":"Crossref","is-referenced-by-count":24,"title":["KORP: knowledge-based 6D potential for fast protein and loop modeling"],"prefix":"10.1093","volume":"35","author":[{"given":"Jos\u00e9 Ram\u00f3n","family":"L\u00f3pez-Blanco","sequence":"first","affiliation":[{"name":"Rocasolano Institute of Physical Chemistry C.S.I.C Department of Biological Chemical Physics, , Madrid, Spain"}]},{"given":"Pablo","family":"Chac\u00f3n","sequence":"additional","affiliation":[{"name":"Rocasolano Institute of Physical Chemistry C.S.I.C Department of Biological Chemical Physics, , Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,1,14]]},"reference":[{"key":"2023062711302018500_btz026-B1","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/S1359-0278(96)00051-X","article-title":"Coordination geometry of nonbonded residues in globular proteins","volume":"1","author":"Bahar","year":"1996","journal-title":"Fold. 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