{"id":"https://openalex.org/W4399893452","doi":"https://doi.org/10.1038/s42256-024-00855-1","title":"Multiscale topology-enabled structure-to-sequence transformer for protein\u2013ligand interaction predictions","display_name":"Multiscale topology-enabled structure-to-sequence transformer for protein\u2013ligand interaction predictions","publication_year":2024,"publication_date":"2024-06-21","ids":{"openalex":"https://openalex.org/W4399893452","doi":"https://doi.org/10.1038/s42256-024-00855-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/40718138"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00855-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-024-00855-1","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12290916/pdf/nihms-2098110.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Dong Chen","orcid":"https://orcid.org/0000-0001-5397-0447"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Chen","raw_affiliation_strings":["Department of Mathematics, Michigan State University, East Lansing, MI, USA"],"raw_orcid":"https://orcid.org/0000-0001-5397-0447","affiliations":[{"raw_affiliation_string":"Department of Mathematics, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119767598","display_name":"Jian Liu","orcid":"https://orcid.org/0000-0003-4362-5273"},"institutions":[{"id":"https://openalex.org/I50632499","display_name":"Chongqing University of Technology","ror":"https://ror.org/04vgbd477","country_code":"CN","type":"education","lineage":["https://openalex.org/I50632499"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian Liu","raw_affiliation_strings":["Mathematical Science Research Center, Chongqing University of Technology, Chongqing, China"],"raw_orcid":"https://orcid.org/0000-0003-4362-5273","affiliations":[{"raw_affiliation_string":"Mathematical Science Research Center, Chongqing University of Technology, Chongqing, China","institution_ids":["https://openalex.org/I50632499"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114375564","display_name":"Guo\u2010Wei Wei","orcid":"https://orcid.org/0000-0001-8132-5998"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Guo-Wei Wei","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA","Department of Mathematics, Michigan State University, East Lansing, MI, USA"],"raw_orcid":"https://orcid.org/0000-0001-8132-5998","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Mathematics, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5114375564","https://openalex.org/A5119767598"],"corresponding_institution_ids":["https://openalex.org/I50632499","https://openalex.org/I87216513"],"apc_list":{"value":11690,"currency":"USD","value_usd":11690},"apc_paid":null,"fwci":12.6236,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.99208689,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"6","issue":"7","first_page":"799","last_page":"810"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9988999962806702,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9988999962806702,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976999759674072,"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":0.9975000023841858,"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":0.5462214946746826},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5444196462631226},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5039729475975037},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4038260579109192},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3827791213989258},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19912651181221008},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.16135379672050476},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16036510467529297},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.08783593773841858},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.05343109369277954}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5462214946746826},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5444196462631226},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5039729475975037},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4038260579109192},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3827791213989258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19912651181221008},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.16135379672050476},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16036510467529297},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.08783593773841858},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.05343109369277954}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/s42256-024-00855-1","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s42256-024-00855-1","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},{"id":"pmid:40718138","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40718138","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":"Nature machine intelligence","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12290916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12290916","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12290916/pdf/nihms-2098110.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Mach Intell","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12290916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12290916","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12290916/pdf/nihms-2098110.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Mach Intell","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1048490812","display_name":null,"funder_award_id":"R35GM148196","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2551507366","display_name":null,"funder_award_id":"R35GM148196","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4189064270","display_name":null,"funder_award_id":"R01GM126189","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5117234996","display_name":null,"funder_award_id":"R01 GM126189","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6065440738","display_name":null,"funder_award_id":"65109","funder_id":"https://openalex.org/F4320307115","funder_display_name":"Bristol-Myers Squibb"},{"id":"https://openalex.org/G6765076800","display_name":null,"funder_award_id":"R01AI164266","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G754965114","display_name":null,"funder_award_id":"IIS-1900473","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G965062884","display_name":null,"funder_award_id":"R01 AI164266","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320307115","display_name":"Bristol-Myers Squibb","ror":"https://ror.org/00gtmwv55"},{"id":"https://openalex.org/F4320310016","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332431","display_name":"College of Engineering, Michigan State University","ror":"https://ror.org/05hs6h993"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4399893452.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W1986240377","https://openalex.org/W1993403967","https://openalex.org/W2002243081","https://openalex.org/W2013085020","https://openalex.org/W2025796118","https://openalex.org/W2040643942","https://openalex.org/W2050456292","https://openalex.org/W2112411768","https://openalex.org/W2114162221","https://openalex.org/W2134967712","https://openalex.org/W2144044408","https://openalex.org/W2154670681","https://openalex.org/W2550887636","https://openalex.org/W2578119541","https://openalex.org/W2781821160","https://openalex.org/W2801991413","https://openalex.org/W2806834952","https://openalex.org/W2889677957","https://openalex.org/W2902812092","https://openalex.org/W2911947907","https://openalex.org/W2912171584","https://openalex.org/W2951676304","https://openalex.org/W2963833291","https://openalex.org/W2971801381","https://openalex.org/W2980234582","https://openalex.org/W3001282080","https://openalex.org/W3009499476","https://openalex.org/W3013843370","https://openalex.org/W3015572666","https://openalex.org/W3033534833","https://openalex.org/W3080588469","https://openalex.org/W3082042165","https://openalex.org/W3109549311","https://openalex.org/W3112717538","https://openalex.org/W3118091546","https://openalex.org/W3130189352","https://openalex.org/W3135935512","https://openalex.org/W3157078379","https://openalex.org/W3162155458","https://openalex.org/W3172303648","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3188589934","https://openalex.org/W3195375135","https://openalex.org/W3209909976","https://openalex.org/W3214234430","https://openalex.org/W3216686093","https://openalex.org/W4206018883","https://openalex.org/W4206912588","https://openalex.org/W4210716706","https://openalex.org/W4223481922","https://openalex.org/W4224230705","https://openalex.org/W4226278401","https://openalex.org/W4280538744","https://openalex.org/W4281740412","https://openalex.org/W4289518623","https://openalex.org/W4313156423","https://openalex.org/W4319792726","https://openalex.org/W4322422874","https://openalex.org/W4323306378","https://openalex.org/W4327550249","https://openalex.org/W4379932151","https://openalex.org/W4383099422","https://openalex.org/W4387426831","https://openalex.org/W4387673203","https://openalex.org/W4391256965","https://openalex.org/W4391889225","https://openalex.org/W6739901393","https://openalex.org/W6967503942"],"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/W4396696052"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":33},{"year":2024,"cited_by_count":6}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
