{"id":"https://openalex.org/W4416717573","doi":"https://doi.org/10.1021/acs.jcim.5c02385","title":"Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning","display_name":"Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning","publication_year":2025,"publication_date":"2025-11-26","ids":{"openalex":"https://openalex.org/W4416717573","doi":"https://doi.org/10.1021/acs.jcim.5c02385","pmid":"https://pubmed.ncbi.nlm.nih.gov/41295751"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02385","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02385","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088344760","display_name":"Qiuyi Lyu","orcid":"https://orcid.org/0000-0002-0104-9549"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210105760","display_name":"Frontier Science Foundation","ror":"https://ror.org/01e92na05","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210105760"]}],"countries":["CH","CN"],"is_corresponding":false,"raw_author_name":"Qiuyi Lyu","raw_affiliation_strings":["MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","Shandong University","MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China"],"raw_orcid":"https://orcid.org/0000-0002-0104-9549","affiliations":[{"raw_affiliation_string":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","institution_ids":["https://openalex.org/I4210105760"]},{"raw_affiliation_string":"Shandong University","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103264464","display_name":"Hong Wei","orcid":"https://orcid.org/0000-0002-2361-8589"},"institutions":[{"id":"https://openalex.org/I5740404","display_name":"Tianjin Medical University","ror":"https://ror.org/02mh8wx89","country_code":"CN","type":"education","lineage":["https://openalex.org/I5740404"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Wei","raw_affiliation_strings":["Department of Bioinformatics, School of Basic Medical Sciences","Tianjin Medical University","Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, School of Basic Medical Sciences","institution_ids":[]},{"raw_affiliation_string":"Tianjin Medical University","institution_ids":["https://openalex.org/I5740404"]},{"raw_affiliation_string":"Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China","institution_ids":["https://openalex.org/I5740404"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084135459","display_name":"Shuaishuai Chen","orcid":"https://orcid.org/0000-0002-5491-6650"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuaishuai Chen","raw_affiliation_strings":["School of Information Science and Engineering","Shandong University","School of Information Science and Engineering, Shandong University, Qingdao 266237, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Shandong University","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Information Science and Engineering, Shandong University, Qingdao 266237, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020435329","display_name":"Zhenling Peng","orcid":"https://orcid.org/0000-0003-0303-6693"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210105760","display_name":"Frontier Science Foundation","ror":"https://ror.org/01e92na05","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210105760"]}],"countries":["CH","CN"],"is_corresponding":true,"raw_author_name":"Zhenling Peng","raw_affiliation_strings":["MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","Shandong University","MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","institution_ids":["https://openalex.org/I4210105760"]},{"raw_affiliation_string":"Shandong University","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao 266237, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107636936","display_name":"Jianyi Yang","orcid":"https://orcid.org/0000-0003-2912-7737"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210105760","display_name":"Frontier Science Foundation","ror":"https://ror.org/01e92na05","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210105760"]}],"countries":["CH","CN"],"is_corresponding":true,"raw_author_name":"Jianyi Yang","raw_affiliation_strings":["MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","Shandong University"],"raw_orcid":"https://orcid.org/0000-0003-2912-7737","affiliations":[{"raw_affiliation_string":"MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences","institution_ids":["https://openalex.org/I4210105760"]},{"raw_affiliation_string":"Shandong University","institution_ids":["https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5020435329","https://openalex.org/A5107636936"],"corresponding_institution_ids":["https://openalex.org/I154099455","https://openalex.org/I4210105760"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3126005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"24","first_page":"13465","last_page":"13477"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.911899983882904,"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":0.911899983882904,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.024900000542402267,"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/T11162","display_name":"Enzyme Structure and Function","score":0.022600000724196434,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.5024999976158142},{"id":"https://openalex.org/keywords/inverse","display_name":"Inverse","score":0.4805999994277954},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4706999957561493},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4652999937534332},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.450300008058548},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4429999887943268},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39800000190734863}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7513999938964844},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.5024999976158142},{"id":"https://openalex.org/C207467116","wikidata":"https://www.wikidata.org/wiki/Q4385666","display_name":"Inverse","level":2,"score":0.4805999994277954},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47519999742507935},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4706999957561493},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4652999937534332},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.450300008058548},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4429999887943268},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39800000190734863},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3635999858379364},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.3546000123023987},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3465000092983246},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.335999995470047},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33090001344680786},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3073999881744385},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2930999994277954},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.2892000079154968},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.273499995470047}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":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":"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02385","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02385","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:41295751","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41295751","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G119665751","display_name":null,"funder_award_id":"ZR2023QF156","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G4189440957","display_name":null,"funder_award_id":"32430063","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4294680834","display_name":null,"funder_award_id":"T2222012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5694550632","display_name":null,"funder_award_id":"2023YFF1204003","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6313107900","display_name":null,"funder_award_id":"T2225007","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/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1911270099","https://openalex.org/W2030517878","https://openalex.org/W2094262711","https://openalex.org/W2102245393","https://openalex.org/W2114459720","https://openalex.org/W2115540209","https://openalex.org/W2128674962","https://openalex.org/W2130479394","https://openalex.org/W2170747616","https://openalex.org/W2767691149","https://openalex.org/W2780263532","https://openalex.org/W2804736431","https://openalex.org/W2950806586","https://openalex.org/W2950954328","https://openalex.org/W3040969795","https://openalex.org/W3146944767","https://openalex.org/W3171007011","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3211795435","https://openalex.org/W3215918380","https://openalex.org/W4220998111","https://openalex.org/W4223581484","https://openalex.org/W4226320411","https://openalex.org/W4288077714","https://openalex.org/W4293475204","https://openalex.org/W4312679951","https://openalex.org/W4327550249","https://openalex.org/W4375858802","https://openalex.org/W4390578919","https://openalex.org/W4391221384","https://openalex.org/W4393305449","https://openalex.org/W4393342758","https://openalex.org/W4396918685","https://openalex.org/W4401463754","https://openalex.org/W4401841344","https://openalex.org/W4404447409","https://openalex.org/W4407150866"],"related_works":[],"abstract_inverted_index":{"Protein":[0],"structure":[1,30,72,92,120],"database":[2,31],"search":[3,121],"has":[4],"become":[5],"increasingly":[6],"challenging":[7],"due":[8],"to":[9,95,114],"the":[10,34,81,129,137,152],"growing":[11],"number":[12],"of":[13,136,142],"experimental":[14],"and":[15,27,51,102],"computational":[16],"structures.":[17],"We":[18],"introduce":[19],"mTM-align2,":[20],"a":[21,45,62,90],"novel":[22],"two-step":[23],"approach":[24],"for":[25,128,140,159],"rapid":[26,91],"accurate":[28],"protein":[29,37],"search.":[32],"In":[33],"first":[35,40],"step,":[36],"structures":[38,143],"are":[39,58,78,148],"transformed":[41],"into":[42],"embeddings":[43,57,77,139,147],"using":[44],"pretrained":[46],"inverse":[47],"folding":[48],"model":[49],"(ESM-IF)":[50],"3D":[52],"Zernike":[53],"polynomials.":[54],"The":[55,86,133],"ESM-IF":[56],"further":[59],"optimized":[60],"through":[61],"contrastive":[63],"learning":[64],"network,":[65],"which":[66],"is":[67,161],"trained":[68],"on":[69,80],"\u223c7":[70],"million":[71],"pairs.":[73],"Structures":[74],"with":[75,124],"similar":[76],"returned":[79],"fly":[82],"in":[83,122],"this":[84],"step.":[85],"second":[87],"step":[88],"employs":[89],"alignment":[93],"program":[94],"refine":[96],"top":[97,130],"candidates,":[98],"ensuring":[99],"high":[100],"precision":[101,127],"producing":[103],"high-quality":[104],"alignments.":[105],"Extensive":[106],"benchmarks":[107],"reveal":[108],"that":[109,145],"mTM-align2":[110,138,160],"performs":[111],"competitively":[112],"compared":[113],"other":[115],"leading":[116],"methods,":[117],"completing":[118],"monomeric":[119],"seconds":[123],"over":[125],"90%":[126],"10":[131],"hits.":[132],"t-SNE":[134],"visualization":[135],"thousands":[141],"demonstrates":[144],"our":[146],"structurally":[149],"informed,":[150],"capturing":[151],"global":[153],"structural":[154],"features.":[155],"A":[156],"web":[157],"server":[158],"accessible":[162],"at":[163],"https://yanglab.qd.sdu.edu.cn/mTM-align/.":[164]},"counts_by_year":[],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-11-27T00:00:00"}