{"id":"https://openalex.org/W2152107372","doi":"https://doi.org/10.1093/bioinformatics/btr009","title":"Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation","display_name":"Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation","publication_year":2010,"publication_date":"2010-01-06","ids":{"openalex":"https://openalex.org/W2152107372","doi":"https://doi.org/10.1093/bioinformatics/btr009","mag":"2152107372","pmid":"https://pubmed.ncbi.nlm.nih.gov/21216772"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr009","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr009","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045938742","display_name":"Yang Cao","orcid":"https://orcid.org/0000-0002-1925-2123"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Cao","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044114823","display_name":"Lin Frank Song","orcid":"https://orcid.org/0000-0002-1854-5215"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Song","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047497779","display_name":"Zhichao Miao","orcid":"https://orcid.org/0000-0002-5777-9815"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhichao Miao","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102787531","display_name":"Yun Hu","orcid":"https://orcid.org/0000-0002-8109-0284"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Hu","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086842371","display_name":"Liqing Tian","orcid":"https://orcid.org/0000-0001-9921-0603"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liqing Tian","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062116814","display_name":"Taijiao Jiang","orcid":"https://orcid.org/0000-0002-6280-6347"},"institutions":[{"id":"https://openalex.org/I4210112540","display_name":"Institute of Biophysics","ror":"https://ror.org/01tyv8576","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112540"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Taijiao Jiang","raw_affiliation_strings":["1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and 2Graduate University of Chinese Academy of Sciences, Beijing 100039, China","institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5062116814"],"corresponding_institution_ids":["https://openalex.org/I4210112540","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8166,"has_fulltext":false,"cited_by_count":73,"citation_normalized_percentile":{"value":0.72651985,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"27","issue":"6","first_page":"785","last_page":"790"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.017500000074505806,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.010400000028312206,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.8024424910545349},{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.7138659954071045},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7022082805633545},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6472024321556091},{"id":"https://openalex.org/keywords/relaxation","display_name":"Relaxation (psychology)","score":0.47851479053497314},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42006444931030273},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3029240667819977},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.14551153779029846},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09345638751983643}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.8024424910545349},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.7138659954071045},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7022082805633545},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6472024321556091},{"id":"https://openalex.org/C2776029896","wikidata":"https://www.wikidata.org/wiki/Q3935810","display_name":"Relaxation (psychology)","level":2,"score":0.47851479053497314},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42006444931030273},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3029240667819977},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.14551153779029846},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09345638751983643},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btr009","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr009","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21216772","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21216772","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1574312817","https://openalex.org/W1757046366","https://openalex.org/W1968657531","https://openalex.org/W1970157506","https://openalex.org/W1972728295","https://openalex.org/W1974130578","https://openalex.org/W1977689937","https://openalex.org/W1981029038","https://openalex.org/W1985204165","https://openalex.org/W1988912575","https://openalex.org/W1992426410","https://openalex.org/W1999727368","https://openalex.org/W2012231377","https://openalex.org/W2013238066","https://openalex.org/W2015403140","https://openalex.org/W2024469135","https://openalex.org/W2025786614","https://openalex.org/W2027189612","https://openalex.org/W2028079384","https://openalex.org/W2028843689","https://openalex.org/W2033261728","https://openalex.org/W2039388179","https://openalex.org/W2049659492","https://openalex.org/W2050064341","https://openalex.org/W2088608587","https://openalex.org/W2089555384","https://openalex.org/W2092147656","https://openalex.org/W2093332609","https://openalex.org/W2101712920","https://openalex.org/W2106648157","https://openalex.org/W2108505331","https://openalex.org/W2108627006","https://openalex.org/W2122211218","https://openalex.org/W2122451172","https://openalex.org/W2125056225","https://openalex.org/W2130479394","https://openalex.org/W2141685906","https://openalex.org/W2154031461","https://openalex.org/W2156286349","https://openalex.org/W2162166182","https://openalex.org/W2163118761","https://openalex.org/W2164130591","https://openalex.org/W2166317516","https://openalex.org/W2172114588","https://openalex.org/W3020957661"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W2052399476","https://openalex.org/W2810163160","https://openalex.org/W2037964119","https://openalex.org/W1494829770","https://openalex.org/W4220905048","https://openalex.org/W4385077663","https://openalex.org/W2064314890"],"abstract_inverted_index":{"MOTIVATION:":[0],"Side-chain":[1],"modeling":[2,16,57,88],"has":[3],"seen":[4],"wide":[5],"applications":[6],"in":[7,31],"computational":[8,108],"structure":[9],"biology.":[10],"Most":[11],"of":[12,36,75],"the":[13,19,32,49,84],"popular":[14,86],"side-chain":[15,56,87,121],"programs":[17],"explore":[18],"conformation":[20],"space":[21,73],"using":[22],"discrete":[23],"rigid":[24],"rotamers":[25,76],"for":[26,119],"speed":[27],"and":[28,47,97],"efficiency.":[29],"However,":[30],"tightly":[33],"packed":[34],"environments":[35],"protein":[37],"interiors,":[38],"these":[39],"methods":[40],"will":[41],"inherently":[42],"lead":[43],"to":[44,127],"atomic":[45,92],"clashes":[46,93],"hinder":[48],"prediction":[50,103],"accuracy.":[51],"RESULTS:":[52],"We":[53,110],"present":[54],"a":[55,62,116],"method":[58,118],"(CIS-RR),":[59],"which":[60],"couples":[61],"novel":[63],"clash-detection":[64],"guided":[65],"iterative":[66],"search":[67],"(CIS)":[68],"algorithm":[69],"with":[70,83],"continuous":[71],"torsion":[72],"optimization":[74],"(RR).":[77],"Benchmark":[78],"testing":[79],"shows":[80],"that":[81,112],"compared":[82],"existing":[85],"methods,":[89],"CIS-RR":[90,113,124],"removes":[91],"much":[94],"more":[95],"effectively":[96],"achieves":[98],"comparable":[99,107],"or":[100],"even":[101],"better":[102],"accuracy":[104],"while":[105],"having":[106],"cost.":[109],"believe":[111],"could":[114],"be":[115],"useful":[117],"accurate":[120],"modeling.":[122],"AVAILABILITY:":[123],"is":[125],"available":[126],"non-commercial":[128],"users":[129],"at":[130],"our":[131],"website:":[132],"http://jianglab.ibp.ac.cn/lims/cisrr/cisrr.html.":[133]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
