{"id":"https://openalex.org/W3215415010","doi":"https://doi.org/10.1093/bioinformatics/btab798","title":"Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment","display_name":"Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment","publication_year":2021,"publication_date":"2021-11-19","ids":{"openalex":"https://openalex.org/W3215415010","doi":"https://doi.org/10.1093/bioinformatics/btab798","mag":"3215415010","pmid":"https://pubmed.ncbi.nlm.nih.gov/34849594"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab798","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab798","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/A5109526575","display_name":"Maksim V Shegay","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Maksim V Shegay","raw_affiliation_strings":["Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033744508","display_name":"Vytas K. \u0160vedas","orcid":"https://orcid.org/0000-0002-1664-0307"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vytas K \u0160vedas","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044421524","display_name":"Vladimir Voevodin","orcid":"https://orcid.org/0000-0001-6036-5106"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]},{"id":"https://openalex.org/I4210159227","display_name":"Institute of Mathematical Problems of Biology","ror":"https://ror.org/04xtpdj18","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210124601","https://openalex.org/I4210159227"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Vladimir V Voevodin","raw_affiliation_strings":["Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","Research Computing Center, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computing Center, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235","https://openalex.org/I4210159227"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028479633","display_name":"Dmitry Suplatov","orcid":"https://orcid.org/0000-0002-7054-3487"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Dmitry A Suplatov","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia"],"raw_orcid":"https://orcid.org/0000-0002-7054-3487","affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005607792","display_name":"\u041d. \u041d. \u041f\u043e\u043f\u043e\u0432\u0430","orcid":"https://orcid.org/0000-0002-3339-1365"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Nina N Popova","raw_affiliation_strings":["Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Vorobjev Hills , Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5005607792","https://openalex.org/A5028479633"],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4885,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.62897146,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"38","issue":"4","first_page":"985","last_page":"989"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.38999998569488525,"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":0.38999998569488525,"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":0.27459999918937683,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.12229999899864197,"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":0.6761660575866699},{"id":"https://openalex.org/keywords/genetic-algorithm","display_name":"Genetic algorithm","score":0.5886085629463196},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5570940971374512},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.48742154240608215},{"id":"https://openalex.org/keywords/tree-structure","display_name":"Tree structure","score":0.4538685977458954},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3629800081253052},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.23655933141708374},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15597939491271973},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14377334713935852},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.1316954791545868},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.07345882058143616}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6761660575866699},{"id":"https://openalex.org/C8880873","wikidata":"https://www.wikidata.org/wiki/Q187787","display_name":"Genetic algorithm","level":2,"score":0.5886085629463196},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5570940971374512},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.48742154240608215},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.4538685977458954},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3629800081253052},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.23655933141708374},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15597939491271973},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14377334713935852},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.1316954791545868},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.07345882058143616}],"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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab798","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab798","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:34849594","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34849594","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":[{"id":"https://openalex.org/G5016262575","display_name":null,"funder_award_id":"20-07-00970","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"},{"id":"https://openalex.org/G8084587516","display_name":null,"funder_award_id":"18-29-13060","funder_id":"https://openalex.org/F4320321079","funder_display_name":"Russian Foundation for Basic Research"}],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1573534773","https://openalex.org/W1659842140","https://openalex.org/W1794629994","https://openalex.org/W1967538863","https://openalex.org/W1974050623","https://openalex.org/W1980913156","https://openalex.org/W1990771923","https://openalex.org/W2013096383","https://openalex.org/W2023385944","https://openalex.org/W2028624874","https://openalex.org/W2031901496","https://openalex.org/W2043887813","https://openalex.org/W2065921821","https://openalex.org/W2102941368","https://openalex.org/W2126396156","https://openalex.org/W2130060890","https://openalex.org/W2143292980","https://openalex.org/W2146879413","https://openalex.org/W2156909290","https://openalex.org/W2158862451","https://openalex.org/W2161151688","https://openalex.org/W2168239566","https://openalex.org/W2243146974","https://openalex.org/W2572857085","https://openalex.org/W2605897695","https://openalex.org/W2617750324","https://openalex.org/W2730968108","https://openalex.org/W2776264363","https://openalex.org/W2780263532","https://openalex.org/W2898364362","https://openalex.org/W2927518284","https://openalex.org/W2944021648","https://openalex.org/W2946281764","https://openalex.org/W2950873526","https://openalex.org/W2964301053","https://openalex.org/W3016020348","https://openalex.org/W3016533682","https://openalex.org/W3047233668","https://openalex.org/W3093213262","https://openalex.org/W3115809040","https://openalex.org/W3132373268","https://openalex.org/W3135181189","https://openalex.org/W3148480851","https://openalex.org/W3179636787","https://openalex.org/W3203343200","https://openalex.org/W4211255096","https://openalex.org/W4243828423","https://openalex.org/W4300107274","https://openalex.org/W6661317556","https://openalex.org/W6684653327","https://openalex.org/W6762319404"],"related_works":["https://openalex.org/W2093885745","https://openalex.org/W2351266481","https://openalex.org/W2132547887","https://openalex.org/W2516987005","https://openalex.org/W2907786475","https://openalex.org/W2963447120","https://openalex.org/W4289082820","https://openalex.org/W2092152400","https://openalex.org/W2071459461","https://openalex.org/W2963196945"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"the":[2,7,25,32,52,67,89,121,138],"increasing":[3],"availability":[4],"of":[5,9,34,55,63,88,102,109,117,123,128,147],"3D-data,":[6],"focus":[8],"comparative":[10],"bioinformatic":[11],"analysis":[12],"is":[13],"shifting":[14],"from":[15],"protein":[16,57,77,130],"sequence":[17],"alignments":[18],"toward":[19],"more":[20],"content-rich":[21],"3D-alignments.":[22],"This":[23],"raises":[24],"need":[26],"for":[27],"new":[28],"ways":[29],"to":[30,50,83,95,125,136],"improve":[31,51],"accuracy":[33],"3D-superimposition.":[35],"RESULTS:":[36],"We":[37],"proposed":[38],"guide":[39],"tree":[40],"optimization":[41],"with":[42],"genetic":[43],"algorithm":[44],"(GA)":[45],"as":[46,132],"a":[47,61,84],"universal":[48],"tool":[49,135],"alignment":[53,79],"quality":[54,91],"multiple":[56,76],"3D-structures":[58],"systematically.":[59],"As":[60],"proof":[62],"concept,":[64],"we":[65],"implemented":[66],"suggested":[68],"GA-based":[69],"approach":[70],"in":[71,115],"popular":[72],"Matt":[73],"and":[74,104,150],"Caretta":[75],"3D-structure":[78],"(M3DSA)":[80],"algorithms,":[81],"leading":[82],"statistically":[85],"significant":[86],"improvement":[87,114],"TM-score":[90],"indicator":[92],"by":[93],"up":[94],"220-1523%":[96],"on":[97],"'SABmark":[98,105],"Superfamilies'":[99],"(in":[100,107],"49-77%":[101],"cases)":[103,110],"Twilight'":[106],"59-80%":[108],"datasets.":[111],"The":[112,144],"observed":[113],"collections":[116],"distant":[118],"homologies":[119],"highlights":[120],"potentials":[122],"GA":[124],"optimize":[126],"3D-alignments":[127],"diverse":[129],"superfamilies":[131],"one":[133],"plausible":[134],"study":[137],"structure-function":[139],"relationship.":[140],"AVAILABILITY":[141],"AND":[142],"IMPLEMENTATION:":[143],"source":[145],"codes":[146],"patched":[148],"gaCaretta":[149],"gaMatt":[151],"programs":[152],"are":[153,162],"available":[154,163],"open-access":[155],"at":[156,164],"https://github.com/n-canter/gamaps.":[157],"SUPPLEMENTARY":[158],"INFORMATION:":[159],"Supplementary":[160],"data":[161],"Bioinformatics":[165],"online.":[166]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
