{"id":"https://openalex.org/W2949632023","doi":"https://doi.org/10.1093/bioinformatics/btz483","title":"Sequence alignment using machine learning for accurate template-based protein structure prediction","display_name":"Sequence alignment using machine learning for accurate template-based protein structure prediction","publication_year":2019,"publication_date":"2019-06-05","ids":{"openalex":"https://openalex.org/W2949632023","doi":"https://doi.org/10.1093/bioinformatics/btz483","mag":"2949632023","pmid":"https://pubmed.ncbi.nlm.nih.gov/31197318"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz483","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz483","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/A5027016084","display_name":"Shuichiro Makigaki","orcid":"https://orcid.org/0000-0002-1988-2088"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shuichiro Makigaki","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology , Meguro-ku, Tokyo 152-8550, Japan"],"raw_orcid":"https://orcid.org/0000-0002-1988-2088","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology , Meguro-ku, Tokyo 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004756730","display_name":"Takashi Ishida","orcid":"https://orcid.org/0000-0002-9478-3223"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takashi Ishida","raw_affiliation_strings":["Department of Computer Science, School of Computing, Tokyo Institute of Technology , Meguro-ku, Tokyo 152-8550, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Computing, Tokyo Institute of Technology , Meguro-ku, Tokyo 152-8550, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004756730","https://openalex.org/A5027016084"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9114,"has_fulltext":false,"cited_by_count":25,"citation_normalized_percentile":{"value":0.73605957,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"1","first_page":"104","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4422000050544739,"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":0.4422000050544739,"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":0.22540000081062317,"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":0.05420000106096268,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7710871696472168},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7117587327957153},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.6004562973976135},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.59641432762146},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5002682209014893},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.4850408434867859},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4829775393009186},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4652717113494873},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.44606533646583557},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43618059158325195},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.41254425048828125},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.4105416536331177},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3842882812023163},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3652105927467346},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34205883741378784},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18357902765274048},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08051350712776184}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7710871696472168},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7117587327957153},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.6004562973976135},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.59641432762146},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5002682209014893},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.4850408434867859},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4829775393009186},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4652717113494873},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.44606533646583557},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43618059158325195},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.41254425048828125},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.4105416536331177},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3842882812023163},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3652105927467346},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34205883741378784},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18357902765274048},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08051350712776184},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz483","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz483","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:31197318","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31197318","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/G8460544353","display_name":"Structure-based ligand activity prediction using 3-dimensional convolution neural network","funder_award_id":"18K11524","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1964655247","https://openalex.org/W2015292449","https://openalex.org/W2021698020","https://openalex.org/W2037993016","https://openalex.org/W2041338685","https://openalex.org/W2055043387","https://openalex.org/W2055779068","https://openalex.org/W2065283382","https://openalex.org/W2073895233","https://openalex.org/W2085277871","https://openalex.org/W2087064593","https://openalex.org/W2102245393","https://openalex.org/W2109806386","https://openalex.org/W2115540209","https://openalex.org/W2132629607","https://openalex.org/W2139881678","https://openalex.org/W2142827986","https://openalex.org/W2145268834","https://openalex.org/W2147667050","https://openalex.org/W2151031807","https://openalex.org/W2154139219","https://openalex.org/W2158714788","https://openalex.org/W2161072217","https://openalex.org/W2161151688","https://openalex.org/W2163910672","https://openalex.org/W2164255317","https://openalex.org/W2514534732","https://openalex.org/W2557595285","https://openalex.org/W2562171514","https://openalex.org/W2581342503","https://openalex.org/W2606314633","https://openalex.org/W2774178591","https://openalex.org/W2898210859","https://openalex.org/W2949867299","https://openalex.org/W2963457143","https://openalex.org/W6756056205"],"related_works":["https://openalex.org/W2029514038","https://openalex.org/W2051969447","https://openalex.org/W2015399150","https://openalex.org/W2061567716","https://openalex.org/W2009133913","https://openalex.org/W2275032899","https://openalex.org/W2498689255","https://openalex.org/W2075451741","https://openalex.org/W2157930580","https://openalex.org/W2505756865"],"abstract_inverted_index":{"MOTIVATION:":[0],"Template-based":[1],"modeling,":[2],"the":[3,7,38,83,119,129,136],"process":[4],"of":[5,10,40,86,106,142],"predicting":[6],"tertiary":[8,150],"structure":[9,151],"a":[11,61,78,107,115],"protein":[12,16],"by":[13,126,159],"using":[14,82,97],"homologous":[15],"structures,":[17],"is":[18,47,90],"useful":[19],"if":[20],"good":[21],"templates":[22],"can":[23,31],"be":[24],"found.":[25],"Although":[26],"modern":[27],"homology":[28],"detection":[29],"methods":[30],"find":[32],"remote":[33],"homologs":[34],"with":[35,140],"high":[36],"sensitivity,":[37],"accuracy":[39,139],"template-based":[41,72],"models":[42,152],"generated":[43],"from":[44,52,118,156],"homology-detection-based":[45],"alignments":[46,68,96,157],"often":[48],"lower":[49],"than":[50,153],"that":[51,64,141],"ideal":[53],"alignments.":[54],"RESULTS:":[55],"In":[56],"this":[57,111],"study,":[58],"we":[59],"propose":[60],"new":[62],"method":[63,76,112,125,146],"generates":[65,147],"pairwise":[66],"sequence":[67,95,103],"for":[69],"more":[70,148],"accurate":[71,149],"modeling.":[73],"The":[74],"proposed":[75],"trains":[77],"machine":[79,98],"learning":[80],"model":[81],"structural":[84],"alignment":[85],"known":[87],"homologs.":[88],"It":[89],"difficult":[91],"to":[92],"directly":[93],"predict":[94],"learning.":[99],"Thus,":[100],"when":[101],"calculating":[102],"alignments,":[104],"instead":[105],"fixed":[108],"substitution":[109,116],"matrix,":[110],"dynamically":[113],"predicts":[114],"score":[117],"trained":[120],"model.":[121],"We":[122],"evaluate":[123],"our":[124],"carefully":[127],"splitting":[128],"training":[130],"and":[131,134],"test":[132],"datasets":[133],"comparing":[135],"predicted":[137],"structure's":[138],"state-of-the-art":[143],"methods.":[144,161],"Our":[145],"those":[154],"produced":[155],"obtained":[158],"other":[160],"AVAILABILITY":[162],"AND":[163],"IMPLEMENTATION:":[164],"https://github.com/shuichiro-makigaki/exmachina.":[165],"SUPPLEMENTARY":[166],"INFORMATION:":[167],"Supplementary":[168],"data":[169],"are":[170],"available":[171],"at":[172],"Bioinformatics":[173],"online.":[174]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}