{"id":"https://openalex.org/W3215654229","doi":"https://doi.org/10.1093/bib/bbab463","title":"Multi contact-based folding method for<i>de novo</i>protein structure prediction","display_name":"Multi contact-based folding method for<i>de novo</i>protein structure prediction","publication_year":2021,"publication_date":"2021-10-13","ids":{"openalex":"https://openalex.org/W3215654229","doi":"https://doi.org/10.1093/bib/bbab463","mag":"3215654229","pmid":"https://pubmed.ncbi.nlm.nih.gov/34849573"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab463","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab463","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5087388574","display_name":"Minghua Hou","orcid":"https://orcid.org/0009-0006-2081-7941"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minghua Hou","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061624407","display_name":"Chunxiang Peng","orcid":"https://orcid.org/0009-0006-9735-0278"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chunxiang Peng","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023785113","display_name":"Xiaogen Zhou","orcid":"https://orcid.org/0000-0001-6839-1923"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiaogen Zhou","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Hangzhou 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Hangzhou 310023, China","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101534274","display_name":"Biao Zhang","orcid":"https://orcid.org/0000-0002-6289-8878"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Biao Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China","institution_ids":["https://openalex.org/I55712492"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049735973","display_name":"Guijun Zhang","orcid":"https://orcid.org/0000-0002-7815-5884"},"institutions":[{"id":"https://openalex.org/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guijun Zhang","raw_affiliation_strings":["College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China","institution_ids":["https://openalex.org/I55712492"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5049735973"],"corresponding_institution_ids":["https://openalex.org/I55712492"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.148,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.4596292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9986000061035156,"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":0.9986000061035156,"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":0.9919999837875366,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.984499990940094,"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/folding","display_name":"Folding (DSP implementation)","score":0.5749374032020569},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5584784150123596},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5067687630653381},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.46380236744880676},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41179192066192627},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.336868554353714},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1994955837726593},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18646150827407837},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10276669263839722},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.09040948748588562},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0618823766708374},{"id":"https://openalex.org/keywords/structural-engineering","display_name":"Structural engineering","score":0.05421045422554016}],"concepts":[{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5749374032020569},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5584784150123596},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5067687630653381},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.46380236744880676},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41179192066192627},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.336868554353714},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1994955837726593},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18646150827407837},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10276669263839722},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.09040948748588562},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0618823766708374},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.05421045422554016}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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/bib/bbab463","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab463","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34849573","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34849573","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1582390173","display_name":null,"funder_award_id":"2019YFE0126100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2708836668","display_name":null,"funder_award_id":"61773346","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3775454306","display_name":null,"funder_award_id":"62173304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1988695007","https://openalex.org/W1995017064","https://openalex.org/W2033354942","https://openalex.org/W2061042699","https://openalex.org/W2064675550","https://openalex.org/W2097606916","https://openalex.org/W2102864100","https://openalex.org/W2104467962","https://openalex.org/W2114340287","https://openalex.org/W2115213105","https://openalex.org/W2115540209","https://openalex.org/W2119843684","https://openalex.org/W2131774270","https://openalex.org/W2136799255","https://openalex.org/W2145991251","https://openalex.org/W2156125289","https://openalex.org/W2161072217","https://openalex.org/W2161151688","https://openalex.org/W2164583490","https://openalex.org/W2166701319","https://openalex.org/W2170471837","https://openalex.org/W2600704321","https://openalex.org/W2624035516","https://openalex.org/W2765742208","https://openalex.org/W2769882797","https://openalex.org/W2778001245","https://openalex.org/W2790309735","https://openalex.org/W2801109052","https://openalex.org/W2808950571","https://openalex.org/W2891275623","https://openalex.org/W2894584887","https://openalex.org/W2902353954","https://openalex.org/W2944535254","https://openalex.org/W2944959599","https://openalex.org/W2949867299","https://openalex.org/W2951621517","https://openalex.org/W2951639995","https://openalex.org/W2960589734","https://openalex.org/W2963436022","https://openalex.org/W2966057938","https://openalex.org/W2970515102","https://openalex.org/W2971003495","https://openalex.org/W2977360892","https://openalex.org/W2987090428","https://openalex.org/W2994958577","https://openalex.org/W2995531725","https://openalex.org/W2997234557","https://openalex.org/W3034300685","https://openalex.org/W3136751755","https://openalex.org/W3175798418","https://openalex.org/W3178212622","https://openalex.org/W6632673138","https://openalex.org/W6680747242","https://openalex.org/W6767973552"],"related_works":["https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W2976965029","https://openalex.org/W2382178265","https://openalex.org/W2055827177","https://openalex.org/W2072666835","https://openalex.org/W4248706500","https://openalex.org/W1999927713","https://openalex.org/W2939859775","https://openalex.org/W4252654006"],"abstract_inverted_index":{"Meta":[0],"contact,":[1],"which":[2],"combines":[3],"different":[4,68],"contact":[5,11,22,35,44,69,91],"maps":[6,70],"into":[7],"one":[8],"to":[9,76,90],"improve":[10],"prediction":[12,32],"accuracy":[13],"and":[14,93,109,113,118,131,137,168],"effectively":[15],"reduce":[16],"the":[17,39,55,64,110,124,142,148,164,180],"noise":[18],"from":[19],"a":[20,25,49,103,135],"single":[21],"map,":[23],"is":[24,60,71,84,100,155,173],"widely":[26],"used":[27,73],"method.":[28],"However,":[29],"protein":[30,78,97],"structure":[31,79],"using":[33],"meta":[34,125],"cannot":[36],"fully":[37],"exploit":[38],"information":[40,66,92,146],"carried":[41],"by":[42,74,151],"original":[43],"maps.":[45],"In":[46,62,81,140],"this":[47],"work,":[48],"multi":[50],"contact-based":[51,126],"folding":[52],"method":[53],"under":[54],"evolutionary":[56],"algorithm":[57],"framework,":[58],"MultiCFold,":[59,63],"proposed.":[61],"thorough":[65],"of":[67,105,144,161],"directly":[72],"populations":[75],"guide":[77],"folding.":[80,98],"addition,":[82],"noncontact":[83,145],"considered":[85],"as":[86],"an":[87],"effective":[88],"supplement":[89],"can":[94],"further":[95],"assist":[96],"MultiCFold":[99,154,172],"tested":[101],"on":[102,163],"set":[104],"120":[106],"nonredundant":[107],"proteins,":[108],"average":[111,114,129,132,149],"TM-score":[112,130,150],"RMSD":[115,133],"reach":[116],"0.617":[117],"5.815":[119],"\u00c5,":[120],"respectively.":[121],"Compared":[122],"with":[123,157],"method,":[127],"MetaCFold,":[128],"have":[134],"6.62":[136],"8.82%":[138],"improvement.":[139],"particular,":[141],"import":[143],"increases":[147],"6.30%.":[152],"Furthermore,":[153],"compared":[156],"four":[158],"state-of-the-art":[159],"methods":[160,178],"CASP13":[162],"24":[165],"FM":[166],"targets,":[167],"results":[169],"show":[170],"that":[171],"significantly":[174],"better":[175],"than":[176],"other":[177],"after":[179],"full-atom":[181],"relax":[182],"procedure.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2021-12-06T00:00:00"}
