{"id":"https://openalex.org/W4391221384","doi":"https://doi.org/10.1021/acs.jcim.3c01455","title":"TM-search: An Efficient and Effective Tool for Protein Structure Database Search","display_name":"TM-search: An Efficient and Effective Tool for Protein Structure Database Search","publication_year":2024,"publication_date":"2024-01-25","ids":{"openalex":"https://openalex.org/W4391221384","doi":"https://doi.org/10.1021/acs.jcim.3c01455","pmid":"https://pubmed.ncbi.nlm.nih.gov/38270339"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01455","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01455","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/A5100451904","display_name":"Zi Liu","orcid":"https://orcid.org/0000-0002-1353-4461"},"institutions":[{"id":"https://openalex.org/I105991555","display_name":"Jingdezhen Ceramic Institute","ror":"https://ror.org/01d0jcz74","country_code":"CN","type":"education","lineage":["https://openalex.org/I105991555"]},{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zi Liu","raw_affiliation_strings":["Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China","School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China"],"affiliations":[{"raw_affiliation_string":"Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China","institution_ids":["https://openalex.org/I105991555"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101510848","display_name":"Chengxin Zhang","orcid":"https://orcid.org/0000-0001-7290-1324"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengxin Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101541427","display_name":"Qidi Zhang","orcid":"https://orcid.org/0000-0002-6823-6015"},"institutions":[{"id":"https://openalex.org/I105991555","display_name":"Jingdezhen Ceramic Institute","ror":"https://ror.org/01d0jcz74","country_code":"CN","type":"education","lineage":["https://openalex.org/I105991555"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qidi Zhang","raw_affiliation_strings":["Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China"],"affiliations":[{"raw_affiliation_string":"Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China","institution_ids":["https://openalex.org/I105991555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008960436","display_name":"Dong\u2010Jun Yu","orcid":"https://orcid.org/0000-0002-6786-8053"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dong-Jun Yu","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China","institution_ids":["https://openalex.org/I36399199"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008960436","https://openalex.org/A5100354659"],"corresponding_institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315","https://openalex.org/I36399199"],"apc_list":null,"apc_paid":null,"fwci":3.2427,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.9212747,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"64","issue":"3","first_page":"1043","last_page":"1049"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9970999956130981,"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":0.9970999956130981,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9930999875068665,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9887999892234802,"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/computer-science","display_name":"Computer science","score":0.7212228775024414},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6696577072143555},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6421419382095337},{"id":"https://openalex.org/keywords/database-search-engine","display_name":"Database search engine","score":0.5957842469215393},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5713436603546143},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.507042407989502},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49559080600738525},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.4777321517467499},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4710174798965454},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.4686053991317749},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.43662557005882263},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.43540000915527344},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.4335539937019348},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.43154558539390564},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.42700958251953125},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.34959083795547485},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3468437194824219},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.24987423419952393},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.232033371925354},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17681479454040527},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.12500810623168945},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0733342170715332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7212228775024414},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6696577072143555},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6421419382095337},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.5957842469215393},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5713436603546143},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.507042407989502},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49559080600738525},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.4777321517467499},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4710174798965454},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.4686053991317749},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.43662557005882263},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.43540000915527344},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.4335539937019348},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.43154558539390564},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.42700958251953125},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.34959083795547485},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3468437194824219},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.24987423419952393},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.232033371925354},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17681479454040527},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.12500810623168945},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0733342170715332},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"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":"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01455","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01455","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:38270339","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38270339","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/G1702080893","display_name":null,"funder_award_id":"62372234","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G640233089","display_name":null,"funder_award_id":"62076111","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6975977380","display_name":null,"funder_award_id":"BK20201304","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"},{"id":"https://openalex.org/G7719334545","display_name":null,"funder_award_id":"62072243","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8879126380","display_name":null,"funder_award_id":"61772273","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/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1897312405","https://openalex.org/W2030517878","https://openalex.org/W2097606916","https://openalex.org/W2097642323","https://openalex.org/W2100494857","https://openalex.org/W2101569554","https://openalex.org/W2102245393","https://openalex.org/W2106433904","https://openalex.org/W2115540209","https://openalex.org/W2125890008","https://openalex.org/W2138116388","https://openalex.org/W2145358391","https://openalex.org/W2158714788","https://openalex.org/W2161072217","https://openalex.org/W2161151688","https://openalex.org/W2611792444","https://openalex.org/W2620998958","https://openalex.org/W2780263532","https://openalex.org/W2920919814","https://openalex.org/W2950806586","https://openalex.org/W2951149542","https://openalex.org/W2953360940","https://openalex.org/W2954851300","https://openalex.org/W2994675673","https://openalex.org/W3211795435","https://openalex.org/W4210840673","https://openalex.org/W4220998111","https://openalex.org/W4226320411","https://openalex.org/W4235848672","https://openalex.org/W4375858802"],"related_works":["https://openalex.org/W2146442590","https://openalex.org/W3016550772","https://openalex.org/W1979707045","https://openalex.org/W2181530468","https://openalex.org/W4206949911","https://openalex.org/W2185518315","https://openalex.org/W3171039768","https://openalex.org/W2593264178","https://openalex.org/W2560155458","https://openalex.org/W2039679484"],"abstract_inverted_index":{"The":[0],"quickly":[1],"increasing":[2],"size":[3],"of":[4,47,97],"the":[5,63],"Protein":[6],"Data":[7],"Bank":[8],"is":[9,60,80,103],"challenging":[10],"biologists":[11],"to":[12,94],"develop":[13],"a":[14,44,52,70,85],"more":[15,106],"scalable":[16],"protein":[17,28,54],"structure":[18,23,29,55,65],"alignment":[19,66],"tool":[20],"for":[21,39],"fast":[22],"database":[24,88],"search.":[25],"Although":[26],"many":[27],"search":[30,56,89],"algorithms":[31],"and":[32,37,69,115],"programs":[33,110],"have":[34],"been":[35],"designed":[36],"implemented":[38],"this":[40],"purpose,":[41],"most":[42],"require":[43],"large":[45],"amount":[46],"computational":[48],"time.":[49],"We":[50],"propose":[51],"novel":[53],"approach,":[57],"TM-search,":[58],"which":[59,102],"based":[61],"on":[62],"pairwise":[64],"program":[67],"TM-align":[68,86],"new":[71],"iterative":[72],"clustering":[73],"algorithm.":[74],"Benchmark":[75],"tests":[76],"demonstrate":[77],"that":[78],"TM-search":[79],"27":[81],"times":[82,105],"faster":[83],"than":[84,107],"full":[87],"while":[90],"still":[91],"being":[92],"able":[93],"identify":[95],"\u223c90%":[96],"all":[98],"high":[99],"TM-score":[100],"hits,":[101],"2-10":[104],"other":[108],"existing":[109],"such":[111],"as":[112],"Foldseek,":[113],"Dali,":[114],"PSI-BLAST.":[116]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
