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Despite these efforts, development of an effective scoring function that can achieve both good accuracy and fast speed still presents a grand challenge.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Based on a coarse-grained representation of a protein structure by using only four main-chain atoms: N, C\u03b1, C and O, we develop a knowledge-based scoring function, called NCACO-score, that integrates different structural information to rapidly model protein structure from sequence. In testing on the Decoys'R'Us sets, we found that NCACO-score can effectively recognize native conformers from their decoys. Furthermore, we demonstrate that NCACO-score can effectively guide fragment assembly for protein structure prediction, which has achieved a good performance in building the structure models for hard targets from CASP8 in terms of both accuracy and speed.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Although NCACO-score is developed based on a coarse-grained model, it is able to discriminate native conformers from decoy conformers with high accuracy. NCACO is a very effective scoring function for structure modeling.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-208","type":"journal-article","created":{"date-parts":[[2011,5,26]],"date-time":"2011-05-26T18:14:22Z","timestamp":1306433662000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["NCACO-score: An effective main-chain dependent scoring function for structure modeling"],"prefix":"10.1186","volume":"12","author":[{"given":"Liqing","family":"Tian","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aiping","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Cao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoxi","family":"Dong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yun","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,5,26]]},"reference":[{"issue":"4","key":"4591_CR1","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1002\/1097-0282(2000)56:4<232::AID-BIP10037>3.0.CO;2-H","volume":"56","author":"TE Cheatham","year":"2000","unstructured":"Cheatham TE, Young MA: Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. 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