{"id":"https://openalex.org/W4210535996","doi":"https://doi.org/10.1093/bioinformatics/btac053","title":"SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model","display_name":"SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model","publication_year":2022,"publication_date":"2022-01-26","ids":{"openalex":"https://openalex.org/W4210535996","doi":"https://doi.org/10.1093/bioinformatics/btac053","pmid":"https://pubmed.ncbi.nlm.nih.gov/35104320"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/7/1888/49010510/btac053.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/38/7/1888/49010510/btac053.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100714940","display_name":"Jaspreet Singh","orcid":"https://orcid.org/0000-0003-4974-5188"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jaspreet Singh","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048999222","display_name":"Thomas Litfin","orcid":"https://orcid.org/0000-0002-4863-3865"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas Litfin","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013626970","display_name":"Jaswinder Singh","orcid":"https://orcid.org/0000-0002-0478-5533"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jaswinder Singh","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046089538","display_name":"Kuldip K. Paliwal","orcid":"https://orcid.org/0000-0002-3553-3662"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Kuldip Paliwal","raw_affiliation_strings":["Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University , Brisbane, QLD 4111, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032724151","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0002-9958-5699"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]},{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]},{"id":"https://openalex.org/I4210128628","display_name":"Peking University Shenzhen Hospital","ror":"https://ror.org/03kkjyb15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128628"]}],"countries":["AU","CN"],"is_corresponding":true,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute for Glycomics, Griffith University , Southport, QLD 4222, Australia","Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518055, China","Peking University Shenzhen Graduate School , Shenzhen 518055, China"],"affiliations":[{"raw_affiliation_string":"Institute for Glycomics, Griffith University , Southport, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518055, China","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Peking University Shenzhen Graduate School , Shenzhen 518055, China","institution_ids":["https://openalex.org/I4210128628"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032724151","https://openalex.org/A5046089538","https://openalex.org/A5100714940"],"corresponding_institution_ids":["https://openalex.org/I11701301","https://openalex.org/I4210102541","https://openalex.org/I4210128628"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.34,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.95702246,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"38","issue":"7","first_page":"1888","last_page":"1894"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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/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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9868000149726868,"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/transformer","display_name":"Transformer","score":0.644080400466919},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5946880578994751},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.49498289823532104},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4335748553276062},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35723966360092163},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1457509994506836},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12683415412902832},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.11211097240447998},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.10677951574325562},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08306828141212463}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.644080400466919},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5946880578994751},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.49498289823532104},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4335748553276062},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35723966360092163},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1457509994506836},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12683415412902832},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.11211097240447998},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.10677951574325562},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08306828141212463}],"mesh":[{"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/7/1888/49010510/btac053.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:35104320","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35104320","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:9113311","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9113311","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/418221","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/418221","pdf_url":null,"source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"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":"","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac053","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac053","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/7/1888/49010510/btac053.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/G5321982477","display_name":null,"funder_award_id":"Titan V GPU","funder_id":"https://openalex.org/F4320309480","funder_display_name":"Nvidia"},{"id":"https://openalex.org/G5657866599","display_name":null,"funder_award_id":"DP210101875","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G962820005","display_name":null,"funder_award_id":"S201101001","funder_id":"https://openalex.org/F4320331248","funder_display_name":"Shenzhen Bay Laboratory"}],"funders":[{"id":"https://openalex.org/F4320309480","display_name":"Nvidia","ror":"https://ror.org/03jdj4y14"},{"id":"https://openalex.org/F4320315813","display_name":"Queensland Cyber Infrastructure Foundation","ror":"https://ror.org/03sd43014"},{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4210535996.pdf","grobid_xml":"https://content.openalex.org/works/W4210535996.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2006796203","https://openalex.org/W2048310584","https://openalex.org/W2076048958","https://openalex.org/W2107867854","https://openalex.org/W2114340287","https://openalex.org/W2119843684","https://openalex.org/W2136799255","https://openalex.org/W2141885858","https://openalex.org/W2557595285","https://openalex.org/W2574496196","https://openalex.org/W2791790018","https://openalex.org/W2801109052","https://openalex.org/W2808950571","https://openalex.org/W2898320067","https://openalex.org/W2905446269","https://openalex.org/W2913820882","https://openalex.org/W2949342052","https://openalex.org/W2949867299","https://openalex.org/W2950954328","https://openalex.org/W2951433247","https://openalex.org/W2953008890","https://openalex.org/W2953524386","https://openalex.org/W2956081200","https://openalex.org/W2963457143","https://openalex.org/W2965837840","https://openalex.org/W2968295962","https://openalex.org/W2971227267","https://openalex.org/W2972411752","https://openalex.org/W2995514860","https://openalex.org/W2999309192","https://openalex.org/W3017657949","https://openalex.org/W3135161193","https://openalex.org/W3160452636","https://openalex.org/W3186340132","https://openalex.org/W4210400672","https://openalex.org/W6686288242","https://openalex.org/W6763868836"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3204019825"],"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":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":14}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
