{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T18:43:53Z","timestamp":1774982633281,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,7]],"date-time":"2020-04-07T00:00:00Z","timestamp":1586217600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM083107"],"award-info":[{"award-number":["GM083107"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM116960"],"award-info":[{"award-number":["GM116960"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI134678"],"award-info":[{"award-number":["AI134678"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI1564756"],"award-info":[{"award-number":["DBI1564756"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS1901191"],"award-info":[{"award-number":["IIS1901191"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Protein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20\u00b0, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3\u2009s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web server, source code and datasets are freely available at https:\/\/zhanglab.ccmb.med.umich.edu\/FASPR and https:\/\/github.com\/tommyhuangthu\/FASPR.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa234","type":"journal-article","created":{"date-parts":[[2020,4,1]],"date-time":"2020-04-01T19:11:43Z","timestamp":1585768303000},"page":"3758-3765","source":"Crossref","is-referenced-by-count":102,"title":["FASPR: an open-source tool for fast and accurate protein side-chain packing"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1005-848X","authenticated-orcid":false,"given":"Xiaoqiang","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"}]},{"given":"Robin","family":"Pearce","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics"},{"name":"Department of Biological Chemistry , University of Michigan, Ann Arbor, MI 48109, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,4,7]]},"reference":[{"key":"2023070101191360800_btaa234-B1","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1016\/j.jmb.2011.02.017","article-title":"Computational protein design and large-scale assessment by I-TASSER structure assembly simulations","volume":"407","author":"Bazzoli","year":"2011","journal-title":"J. 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