{"id":"https://openalex.org/W4413110710","doi":"https://doi.org/10.1093/bioinformatics/btaf425","title":"Beyond the leaderboard: leveraging predictive modeling for protein\u2013ligand insights and discovery","display_name":"Beyond the leaderboard: leveraging predictive modeling for protein\u2013ligand insights and discovery","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4413110710","doi":"https://doi.org/10.1093/bioinformatics/btaf425","pmid":"https://pubmed.ncbi.nlm.nih.gov/40794688"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/8/btaf425/63978884/btaf425.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/8/btaf425/63978884/btaf425.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022063260","display_name":"Dan Kalifa","orcid":"https://orcid.org/0000-0001-6459-6833"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Dan Kalifa","raw_affiliation_strings":["Department of Computer Science, Technion\u2014Israel Institute of Technology , Haifa 3200003,","Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel"],"raw_orcid":"https://orcid.org/0000-0001-6459-6833","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Technion\u2014Israel Institute of Technology , Haifa 3200003,","institution_ids":["https://openalex.org/I174306211"]},{"raw_affiliation_string":"Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029708595","display_name":"Kira Radinsky","orcid":"https://orcid.org/0009-0007-7918-2204"},"institutions":[{"id":"https://openalex.org/I174306211","display_name":"Technion \u2013 Israel Institute of Technology","ror":"https://ror.org/03qryx823","country_code":"IL","type":"education","lineage":["https://openalex.org/I174306211"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Kira Radinsky","raw_affiliation_strings":["Department of Computer Science, Technion\u2014Israel Institute of Technology , Haifa 3200003,","Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Technion\u2014Israel Institute of Technology , Haifa 3200003,","institution_ids":["https://openalex.org/I174306211"]},{"raw_affiliation_string":"Department of Computer Science, Technion-Israel Institute of Technology, Haifa 3200003, Israel","institution_ids":["https://openalex.org/I174306211"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043228682","display_name":"Eric Horvitz","orcid":"https://orcid.org/0000-0002-8823-0614"},"institutions":[{"id":"https://openalex.org/I1290206253","display_name":"Microsoft (United States)","ror":"https://ror.org/00d0nc645","country_code":"US","type":"company","lineage":["https://openalex.org/I1290206253"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I2801852214","display_name":"University of Washington Medical Center","ror":"https://ror.org/00wbzw723","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2801852214"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Horvitz","raw_affiliation_strings":["Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, WA 98195,","Office of the Chief Scientific Officer, Microsoft , Redmond, WA 14820,","Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, United States","Office of the Chief Scientific Officer, Microsoft, Redmond, WA 14820, United States"],"raw_orcid":"https://orcid.org/0000-0002-8823-0614","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington , Seattle, WA 98195,","institution_ids":["https://openalex.org/I2801852214"]},{"raw_affiliation_string":"Office of the Chief Scientific Officer, Microsoft , Redmond, WA 14820,","institution_ids":["https://openalex.org/I1290206253"]},{"raw_affiliation_string":"Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Office of the Chief Scientific Officer, Microsoft, Redmond, WA 14820, United States","institution_ids":["https://openalex.org/I1290206253"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5022063260"],"corresponding_institution_ids":["https://openalex.org/I174306211"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.4953,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.85284069,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"41","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.31459999084472656,"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":0.31459999084472656,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.2231999933719635,"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":0.16210000216960907,"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/computer-science","display_name":"Computer science","score":0.6775123476982117},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5489622950553894},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4480418264865875},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.42058077454566956},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3511713743209839},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32001763582229614},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23548674583435059},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.190841943025589}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6775123476982117},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5489622950553894},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4480418264865875},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.42058077454566956},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3511713743209839},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32001763582229614},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23548674583435059},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.190841943025589}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/8/btaf425/63978884/btaf425.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40794688","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40794688","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:12342388","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12342388","pdf_url":null,"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":"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/btaf425","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf425","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/8/btaf425/63978884/btaf425.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413110710.pdf","grobid_xml":"https://content.openalex.org/works/W4413110710.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1965909642","https://openalex.org/W1975147762","https://openalex.org/W1993046136","https://openalex.org/W2057260453","https://openalex.org/W2074824035","https://openalex.org/W2089159971","https://openalex.org/W2114005496","https://openalex.org/W2138420748","https://openalex.org/W2148914950","https://openalex.org/W2168745915","https://openalex.org/W2334667939","https://openalex.org/W2463514816","https://openalex.org/W2786142325","https://openalex.org/W2939681516","https://openalex.org/W3111648610","https://openalex.org/W3168430821","https://openalex.org/W3177828909","https://openalex.org/W4225552973","https://openalex.org/W4285293106","https://openalex.org/W4296025738","https://openalex.org/W4327550249","https://openalex.org/W4387687322","https://openalex.org/W4388464011","https://openalex.org/W4408220597","https://openalex.org/W6677073350"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"Ligands":[1],"are":[2,27,183],"biomolecules":[3],"that":[4],"bind":[5],"to":[6,29,75,136],"specific":[7,121],"sites":[8],"on":[9,42,142],"target":[10],"proteins,":[11],"often":[12],"inducing":[13],"conformational":[14],"changes":[15,54],"important":[16],"in":[17,68,91,123,171],"the":[18,50,61,85,101,117,120,128,131],"protein's":[19],"function.":[20],"Knowledge":[21],"about":[22],"ligand":[23,132],"interactions":[24],"with":[25,127,155],"proteins":[26,170],"fundamental":[28],"understanding":[30],"biological":[31,105,143],"mechanisms":[32],"and":[33,46,52,72,79,139,152,166,181],"advancing":[34],"drug":[35],"discovery.":[36],"Traditional":[37],"protein":[38,92,149],"language":[39,150],"models":[40,151],"focus":[41,137],"amino":[43],"acid":[44],"sequences":[45],"3D":[47],"structures,":[48],"overlooking":[49],"structural":[51,167],"functional":[53,165],"induced":[55],"by":[56],"protein-ligand":[57,88],"interactions.":[58],"We":[59,82,99,113],"investigate":[60],"value":[62],"of":[63,87,119,130,169],"integrating":[64],"ligand-protein":[65],"binding":[66],"data":[67,90,182],"several":[69],"predictive":[70,97,124],"challenges":[71],"leverage":[73],"findings":[74],"frame":[76],"research":[77],"directions":[78],"questions.":[80],"RESULTS:":[81],"show":[83],"how":[84,116],"integration":[86],"interaction":[89],"representation":[93],"learning":[94,161],"can":[95,134],"increase":[96],"power.":[98],"evaluate":[100],"methodology":[102],"across":[103],"diverse":[104],"tasks,":[106],"demonstrating":[107],"consistent":[108],"improvements":[109],"over":[110],"state-of-the-art":[111],"models.":[112],"further":[114],"demonstrate":[115],"study":[118],"boosts":[122],"capabilities":[125],"coming":[126],"introduction":[129],"modality":[133],"serve":[135],"attention":[138],"provide":[140],"insights":[141],"mechanisms.":[144],"By":[145],"leveraging":[146],"large":[147],"pretrained":[148],"enriching":[153],"them":[154],"interaction-specific":[156],"features":[157],"through":[158],"a":[159],"tailored":[160],"process,":[162],"we":[163],"capture":[164],"nuances":[168],"their":[172],"biochemical":[173],"context.":[174],"AVAILABILITY":[175],"AND":[176],"IMPLEMENTATION:":[177],"The":[178],"full":[179],"code":[180],"freely":[184],"available":[185],"at":[186],"https://github.com/kalifadan/ProtLigand":[187],"(DOI:":[188],"https://doi.org/10.5281/zenodo.15808053).":[189]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}