{"id":"https://openalex.org/W4308685963","doi":"https://doi.org/10.1093/bioinformatics/btac723","title":"Improving protein structure prediction using templates and sequence embedding","display_name":"Improving protein structure prediction using templates and sequence embedding","publication_year":2022,"publication_date":"2022-11-10","ids":{"openalex":"https://openalex.org/W4308685963","doi":"https://doi.org/10.1093/bioinformatics/btac723","pmid":"https://pubmed.ncbi.nlm.nih.gov/36355462"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac723/48448684/btac723.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac723/48448684/btac723.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081693954","display_name":"Fandi Wu","orcid":"https://orcid.org/0000-0003-1615-3004"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Fandi Wu","raw_affiliation_strings":["Institute of Computing Technology, Chinese Academy of Sciences , Beijing 626011, China","Toyota Technological Institute at Chicago , Chicago, IL 60637, USA","University of Chinese Academy of Sciences , Beijing 100049, China"],"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology, Chinese Academy of Sciences , Beijing 626011, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Toyota Technological Institute at Chicago , Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025240664","display_name":"Xiaoyang Jing","orcid":"https://orcid.org/0000-0001-7193-9101"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoyang Jing","raw_affiliation_strings":["Toyota Technological Institute at Chicago , Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago , Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100426938","display_name":"Xiao Luo","orcid":"https://orcid.org/0000-0002-7987-3714"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Luo","raw_affiliation_strings":["Toyota Technological Institute at Chicago , Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago , Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019398608","display_name":"Jinbo Xu","orcid":"https://orcid.org/0000-0001-7111-4839"},"institutions":[{"id":"https://openalex.org/I160992636","display_name":"Toyota Technological Institute at Chicago","ror":"https://ror.org/02sn5gb64","country_code":"US","type":"education","lineage":["https://openalex.org/I160992636"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinbo Xu","raw_affiliation_strings":["Toyota Technological Institute at Chicago , Chicago, IL 60637, USA"],"affiliations":[{"raw_affiliation_string":"Toyota Technological Institute at Chicago , Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I160992636"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081693954"],"corresponding_institution_ids":["https://openalex.org/I160992636","https://openalex.org/I19820366","https://openalex.org/I4210090176","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9532,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.73671652,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"39","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":0.9995999932289124,"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":0.9995999932289124,"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":0.998199999332428,"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":0.9939000010490417,"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/template","display_name":"Template","score":0.9695122241973877},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.7507592439651489},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6973561644554138},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5756977200508118},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5732477903366089},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44275814294815063},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33101773262023926},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2862703800201416},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08478739857673645}],"concepts":[{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.9695122241973877},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7507592439651489},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6973561644554138},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5756977200508118},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5732477903366089},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44275814294815063},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33101773262023926},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2862703800201416},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08478739857673645},{"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/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac723/48448684/btac723.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36355462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36355462","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},{"id":"pmh:oai:pubmedcentral.nih.gov:9805584","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805584","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac723","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac723","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac723/48448684/btac723.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2229035017","display_name":null,"funder_award_id":"R01GM089753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2802911279","display_name":null,"funder_award_id":"Young","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3027545885","display_name":null,"funder_award_id":"61925208","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3841266055","display_name":null,"funder_award_id":"6222221","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4020255992","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4688678934","display_name":"ABI Development: Developing RaptorX Web Portal for Protein Structure and Functional Study","funder_award_id":"1564955","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5522120177","display_name":null,"funder_award_id":"62222","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6059438410","display_name":null,"funder_award_id":"19252","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7033253288","display_name":null,"funder_award_id":"Grants","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7537392905","display_name":null,"funder_award_id":"62222214","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8014835415","display_name":null,"funder_award_id":"U22A2028","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8185830075","display_name":"Collaborative Research: Exploring the Role of Organics in Atmospheric Contact Nucleation","funder_award_id":"1925208","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8248710231","display_name":"URoL:EN - Rules of Resilience: Predicting transformation of emergent freshwater networks under variable climate regimes","funder_award_id":"2222214","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8589651859","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G8989131803","display_name":null,"funder_award_id":"DBI1564955","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320322847","display_name":"Youth Innovation Promotion Association of the Chinese Academy of Sciences","ror":"https://ror.org/031141b54"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320335892","display_name":"Youth Innovation Promotion Association","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4308685963.pdf","grobid_xml":"https://content.openalex.org/works/W4308685963.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2051210555","https://openalex.org/W2069458148","https://openalex.org/W2102245393","https://openalex.org/W2102461176","https://openalex.org/W2151581834","https://openalex.org/W2557595285","https://openalex.org/W2949867299","https://openalex.org/W2950954328","https://openalex.org/W2953008890","https://openalex.org/W2971733377","https://openalex.org/W2972411752","https://openalex.org/W2980789587","https://openalex.org/W2980805969","https://openalex.org/W2987090428","https://openalex.org/W2995514860","https://openalex.org/W2997234557","https://openalex.org/W2999044305","https://openalex.org/W3159634588","https://openalex.org/W3163965514","https://openalex.org/W3177828909","https://openalex.org/W3198789071","https://openalex.org/W3209492740"],"related_works":["https://openalex.org/W2121300814","https://openalex.org/W4234406076","https://openalex.org/W1886613375","https://openalex.org/W4236081792","https://openalex.org/W4250583430","https://openalex.org/W2010731026","https://openalex.org/W2966686650","https://openalex.org/W3023334178","https://openalex.org/W2036923798","https://openalex.org/W2113993025"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
