{"id":"https://openalex.org/W4200182440","doi":"https://doi.org/10.1021/acs.jcim.1c00836","title":"Predicting Protein\u2013Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment","display_name":"Predicting Protein\u2013Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment","publication_year":2021,"publication_date":"2021-12-21","ids":{"openalex":"https://openalex.org/W4200182440","doi":"https://doi.org/10.1021/acs.jcim.1c00836","pmid":"https://pubmed.ncbi.nlm.nih.gov/34931833"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c00836","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00836","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9020583","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032107354","display_name":"Xianjin Xu","orcid":"https://orcid.org/0000-0002-5011-2997"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xianjin Xu","raw_affiliation_strings":["Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States"],"raw_orcid":"https://orcid.org/0000-0002-5011-2997","affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081082371","display_name":"Xiaoqin Zou","orcid":"https://orcid.org/0000-0003-0637-8648"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaoqin Zou","raw_affiliation_strings":["Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States"],"raw_orcid":"https://orcid.org/0000-0003-0637-8648","affiliations":[{"raw_affiliation_string":"Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081082371"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":3.04,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.92469969,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"62","issue":"1","first_page":"27","last_page":"39"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9979000091552734,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9965000152587891,"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/peptide","display_name":"Peptide","score":0.8425517082214355},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6869560480117798},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5537546277046204},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5141404271125793},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.48785400390625},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44472068548202515},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.41124871373176575},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3335036337375641},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2813435196876526},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2074974775314331}],"concepts":[{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.8425517082214355},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6869560480117798},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5537546277046204},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5141404271125793},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.48785400390625},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44472068548202515},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.41124871373176575},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3335036337375641},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2813435196876526},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2074974775314331},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.1c00836","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c00836","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:34931833","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34931833","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9020583","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9020583","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9020583","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9020583","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1656440795","display_name":null,"funder_award_id":"R35 GM136409","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1975285765","display_name":null,"funder_award_id":"R01 HL126774","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2661217566","display_name":null,"funder_award_id":"R01 GM109980","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2699039349","display_name":null,"funder_award_id":"R01HL142301","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6031133963","display_name":null,"funder_award_id":"R35GM136409","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6057762391","display_name":null,"funder_award_id":"R01GM109980","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6779582418","display_name":null,"funder_award_id":"R01HL126774","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G8147541079","display_name":null,"funder_award_id":"R01 HL142301","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1607931568","https://openalex.org/W1609599771","https://openalex.org/W1768303176","https://openalex.org/W1938743025","https://openalex.org/W1979201508","https://openalex.org/W1992450378","https://openalex.org/W1998624640","https://openalex.org/W2004360551","https://openalex.org/W2006192061","https://openalex.org/W2017793317","https://openalex.org/W2023272942","https://openalex.org/W2030991907","https://openalex.org/W2044730187","https://openalex.org/W2054394841","https://openalex.org/W2054954101","https://openalex.org/W2055905702","https://openalex.org/W2108107014","https://openalex.org/W2114512254","https://openalex.org/W2115133023","https://openalex.org/W2124351063","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134967712","https://openalex.org/W2143094533","https://openalex.org/W2143210482","https://openalex.org/W2233834908","https://openalex.org/W2342678031","https://openalex.org/W2520917239","https://openalex.org/W2566470886","https://openalex.org/W2606532257","https://openalex.org/W2766509651","https://openalex.org/W2799876761","https://openalex.org/W2800677598","https://openalex.org/W2802186587","https://openalex.org/W2948988173","https://openalex.org/W2952059807","https://openalex.org/W2994315623","https://openalex.org/W2996827397","https://openalex.org/W3000230289","https://openalex.org/W4211156111"],"related_works":["https://openalex.org/W2393806059","https://openalex.org/W2143537935","https://openalex.org/W1589975312","https://openalex.org/W3210150956","https://openalex.org/W2582797103","https://openalex.org/W2046677260","https://openalex.org/W1999832194","https://openalex.org/W2073366206","https://openalex.org/W1994459954","https://openalex.org/W1837011314"],"abstract_inverted_index":{"Predicting":[0],"protein-peptide":[1,34,53,66,137],"complex":[2,35],"structures":[3],"is":[4,55,69,272],"crucial":[5],"to":[6,18,82,147],"the":[7,29,62,65,113,117,140,154,172,177,189,238,244,248,264],"understanding":[8],"of":[9,13,47,50,134,153,167,235,261],"a":[10,75,107,129,163,232,258],"vast":[11],"variety":[12],"peptide-mediated":[14],"cellular":[15],"processes":[16],"and":[17,24,43,106,116,180,184,215,221,241],"peptide-based":[19],"drug":[20],"development.":[21],"Peptide":[22],"flexibility":[23],"binding":[25,67],"mode":[26],"ranking":[27],"are":[28,39,121,156],"two":[30,211],"major":[31],"challenges":[32,85],"for":[33,171,188,201,237,243],"structure":[36,120],"prediction.":[37,203],"Peptides":[38],"highly":[40],"flexible":[41,109,182],"molecules,":[42],"therefore,":[44],"brute-force":[45],"modeling":[46],"peptide":[48,114,141],"conformations":[49],"interest":[51],"in":[52,90,99,149],"docking":[54,174,192,240,246],"beyond":[56],"current":[57],"computing":[58],"power.":[59],"Inspired":[60],"by":[61],"fact":[63],"that":[64],"process":[68],"like":[70],"protein":[71,118],"folding,":[72],"we":[73],"developed":[74],"novel":[76],"strategy,":[77,98],"named":[78],"MDockPeP2,":[79],"which":[80,150,217],"tries":[81],"address":[83],"these":[84],"using":[86,128],"physicochemical":[87],"information":[88],"embedded":[89],"abundant":[91],"monomeric":[92],"proteins":[93],"with":[94,101,139,176],"an":[95,102],"exhaustive":[96],"search":[97,105],"combination":[100],"integrated":[103],"global":[104],"local":[108],"minimization":[110],"method.":[111],"Only":[112],"sequence":[115,142],"crystal":[119],"required.":[122],"The":[123,270],"method":[124,230],"was":[125],"systemically":[126],"assessed":[127],"newly":[130],"constructed":[131],"structural":[132],"database":[133],"89":[135],"nonredundant":[136],"complexes":[138],"length":[143],"ranging":[144],"from":[145],"5":[146],"29":[148],"about":[151],"half":[152],"peptides":[155,223],"longer":[157],"than":[158],"15":[159,225],"residues.":[160],"MDockPeP2":[161,204,256],"yielded":[162],"total":[164],"success":[165,208,233,259],"rate":[166,234,260],"58.4%":[168],"(70.8,":[169],"79.8%)":[170],"bound":[173,178,239],"(i.e.,":[175],"receptor":[179],"fully":[181],"peptides)":[183],"19.0%":[185],"(44.8,":[186],"70.7%)":[187],"challenging":[190],"unbound":[191,245],"when":[193,247,263],"top":[194,249,265],"10":[195,250,266],"(100,":[196],"1000)":[197],"models":[198,251,267],"were":[199,252,268],"considered":[200],"each":[202],"achieved":[205,257],"significantly":[206],"higher":[207],"rates":[209],"on":[210],"other":[212],"datasets,":[213],"peptiDB":[214],"LEADS-PEP,":[216,255],"contain":[218],"only":[219],"short-":[220],"medium-size":[222],"(\u2264":[224],"residues).":[226],"For":[227,254],"peptiDB,":[228],"our":[229],"obtained":[231],"62.0%":[236],"35.9%":[242],"considered.":[253,269],"69.8%":[262],"program":[271],"available":[273],"at":[274],"https://zougrouptoolkit.missouri.edu/mdockpep2/download.html.":[275]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}