{"id":"https://openalex.org/W4388044321","doi":"https://doi.org/10.1177/10943420231201151","title":"TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences","display_name":"TwoFold: Highly accurate structure and affinity prediction for protein-ligand complexes from sequences","publication_year":2023,"publication_date":"2023-10-30","ids":{"openalex":"https://openalex.org/W4388044321","doi":"https://doi.org/10.1177/10943420231201151"},"language":"en","primary_location":{"id":"doi:10.1177/10943420231201151","is_oa":false,"landing_page_url":"https://doi.org/10.1177/10943420231201151","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/servlets/purl/2205431","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053937845","display_name":"Darren J. Hsu","orcid":"https://orcid.org/0000-0002-0353-7626"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Darren J Hsu","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058248684","display_name":"Hao Lu","orcid":"https://orcid.org/0000-0001-8941-870X"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Lu","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051291589","display_name":"Aditya Kashi","orcid":"https://orcid.org/0000-0003-2589-3792"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aditya Kashi","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012951247","display_name":"Michael A. Matheson","orcid":"https://orcid.org/0000-0003-1512-5255"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Matheson","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018744978","display_name":"John Gounley","orcid":null},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Gounley","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101916963","display_name":"Feiyi Wang","orcid":"https://orcid.org/0000-0002-0099-1559"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Feiyi Wang","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062940770","display_name":"Wayne Joubert","orcid":"https://orcid.org/0000-0003-4771-998X"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wayne Joubert","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023856625","display_name":"Jens Gl\u00e4ser","orcid":"https://orcid.org/0000-0003-1852-3849"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jens Glaser","raw_affiliation_strings":["National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5023856625"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":null,"apc_paid":null,"fwci":0.7697,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.73605168,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"37","issue":"6","first_page":"666","last_page":"682"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9947999715805054,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9907000064849854,"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/protein-ligand","display_name":"Protein ligand","score":0.5491412878036499},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4977774918079376},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4882552921772003},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4643462300300598},{"id":"https://openalex.org/keywords/solver","display_name":"Solver","score":0.44772815704345703},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4363977909088135},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.42716917395591736},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.36646974086761475},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3288545608520508},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3230288326740265},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21695685386657715},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0753297507762909}],"concepts":[{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5491412878036499},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4977774918079376},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4882552921772003},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4643462300300598},{"id":"https://openalex.org/C2778770139","wikidata":"https://www.wikidata.org/wiki/Q1966904","display_name":"Solver","level":2,"score":0.44772815704345703},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4363977909088135},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.42716917395591736},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36646974086761475},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3288545608520508},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3230288326740265},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21695685386657715},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0753297507762909},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/10943420231201151","is_oa":false,"landing_page_url":"https://doi.org/10.1177/10943420231201151","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:osti.gov:2205431","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2205431","pdf_url":"https://www.osti.gov/servlets/purl/2205431","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:2205431","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2205431","pdf_url":"https://www.osti.gov/servlets/purl/2205431","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"score":0.44999998807907104,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388044321.pdf"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1992156271","https://openalex.org/W2017254234","https://openalex.org/W2559655401","https://openalex.org/W2612690371","https://openalex.org/W2666522191","https://openalex.org/W2752879223","https://openalex.org/W2769423117","https://openalex.org/W2902812092","https://openalex.org/W2923764619","https://openalex.org/W3016776150","https://openalex.org/W3040739508","https://openalex.org/W3138526880","https://openalex.org/W3149818211","https://openalex.org/W3155545561","https://openalex.org/W3158755582","https://openalex.org/W3176005660","https://openalex.org/W3177828909","https://openalex.org/W3189646261","https://openalex.org/W3192713004","https://openalex.org/W3202105508","https://openalex.org/W3203459683","https://openalex.org/W3207663361","https://openalex.org/W3211795435","https://openalex.org/W3212324398","https://openalex.org/W3215574293","https://openalex.org/W3216878690","https://openalex.org/W4212774754","https://openalex.org/W4220990251","https://openalex.org/W4221152951","https://openalex.org/W4224231763","https://openalex.org/W4226001818","https://openalex.org/W4250310797","https://openalex.org/W4281701642","https://openalex.org/W4300166936","https://openalex.org/W4303478269","https://openalex.org/W4321636633","https://openalex.org/W6605100834","https://openalex.org/W6816612408"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2043066834","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W1564749278","https://openalex.org/W2294851134","https://openalex.org/W3215498386"],"abstract_inverted_index":{"We":[0],"describe":[1],"our":[2],"development":[3],"of":[4],"ab":[5],"initio":[6],"protein-ligand":[7],"binding":[8,16],"pose":[9],"prediction":[10,18],"models":[11,19,34,50],"based":[12,20],"on":[13,21,64],"transformers":[14],"and":[15,30,37],"affinity":[17],"the":[22,32],"neural":[23],"tangent":[24],"kernel":[25],"(NTK).":[26],"Folding":[27],"both":[28],"protein":[29,46],"ligand,":[31],"TwoFold":[33],"achieve":[35],"efficient":[36],"quality":[38],"predictions":[39],"matching":[40],"state-of-the-art":[41],"implementations":[42],"while":[43],"additionally":[44],"reconstructing":[45],"structures.":[47],"Solving":[48],"NTK":[49],"points":[51],"to":[52],"a":[53],"new":[54],"use":[55],"case":[56],"for":[57],"highly":[58],"optimized":[59],"linear":[60],"solver":[61],"benchmarking":[62],"codes":[63],"HPC.":[65]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
