{"id":"https://openalex.org/W4387692774","doi":"https://doi.org/10.1021/acs.jcim.3c00722","title":"Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method","display_name":"Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method","publication_year":2023,"publication_date":"2023-10-17","ids":{"openalex":"https://openalex.org/W4387692774","doi":"https://doi.org/10.1021/acs.jcim.3c00722","pmid":"https://pubmed.ncbi.nlm.nih.gov/37847557"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00722","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00722","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://escholarship.org/content/qt77x0s1bx/qt77x0s1bx.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039222986","display_name":"Garrett A. Stevenson","orcid":"https://orcid.org/0000-0001-7085-8334"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Garrett A. Stevenson","raw_affiliation_strings":["Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":"https://orcid.org/0000-0001-7085-8334","affiliations":[{"raw_affiliation_string":"Computational Engineering Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088463356","display_name":"Daniel Kirshner","orcid":"https://orcid.org/0000-0002-1293-9969"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan Kirshner","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038376296","display_name":"Brian J. Bennion","orcid":"https://orcid.org/0000-0002-2761-5190"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian J. Bennion","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058777008","display_name":"Yue Yang","orcid":"https://orcid.org/0000-0001-5670-9551"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Yang","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100439355","display_name":"Xiaohua Zhang","orcid":"https://orcid.org/0000-0003-0102-6352"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohua Zhang","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083445132","display_name":"Adam Zem\u0142a","orcid":"https://orcid.org/0000-0003-0504-8647"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adam Zemla","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104034665","display_name":"Marisa W. Torres","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marisa W. Torres","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065438402","display_name":"Aidan Epstein","orcid":"https://orcid.org/0000-0003-3665-6012"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aidan Epstein","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020229955","display_name":"Derek Jones","orcid":"https://orcid.org/0000-0002-9510-6662"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek Jones","raw_affiliation_strings":["Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States","Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":"https://orcid.org/0000-0002-9510-6662","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, United States","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100439155","display_name":"Hyojin Kim","orcid":"https://orcid.org/0000-0001-8690-5617"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyojin Kim","raw_affiliation_strings":["Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077574182","display_name":"William F. Bennett","orcid":"https://orcid.org/0000-0003-3993-9077"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. F. Drew Bennett","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":"https://orcid.org/0000-0003-3993-9077","affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112914666","display_name":"Sergio Wong","orcid":null},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergio E. Wong","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035849909","display_name":"Jonathan Allen","orcid":"https://orcid.org/0000-0002-4359-8263"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan E. Allen","raw_affiliation_strings":["Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":"https://orcid.org/0000-0002-4359-8263","affiliations":[{"raw_affiliation_string":"Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020056606","display_name":"Felice C. Lightstone","orcid":"https://orcid.org/0000-0003-1465-426X"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Felice C. Lightstone","raw_affiliation_strings":["Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5020056606","https://openalex.org/A5039222986"],"corresponding_institution_ids":["https://openalex.org/I1282311441"],"apc_list":null,"apc_paid":null,"fwci":1.35,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.84107726,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"63","issue":"21","first_page":"6655","last_page":"6666"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9952999949455261,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.7538533210754395},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7215069532394409},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.6572540402412415},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5976555943489075},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5816686153411865},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5590949058532715},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.488574355840683},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4720778465270996},{"id":"https://openalex.org/keywords/human-proteome-project","display_name":"Human proteome project","score":0.47153908014297485},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.46660611033439636},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4528130888938904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4244334399700165},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.4150086045265198},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4105088710784912},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3122653365135193},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.28777018189430237},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.25362083315849304},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2044433355331421},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16445839405059814},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15546295046806335},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.07099589705467224}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7538533210754395},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7215069532394409},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.6572540402412415},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5976555943489075},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5816686153411865},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5590949058532715},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.488574355840683},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4720778465270996},{"id":"https://openalex.org/C94795543","wikidata":"https://www.wikidata.org/wiki/Q3813754","display_name":"Human proteome project","level":4,"score":0.47153908014297485},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.46660611033439636},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4528130888938904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4244334399700165},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.4150086045265198},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4105088710784912},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3122653365135193},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28777018189430237},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.25362083315849304},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2044433355331421},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16445839405059814},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15546295046806335},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.07099589705467224},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1021/acs.jcim.3c00722","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00722","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:37847557","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37847557","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt77x0s1bx","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/77x0s1bx","pdf_url":"https://escholarship.org/content/qt77x0s1bx/qt77x0s1bx.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 63, iss 21","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10647021","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10647021","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10647021/pdf/ci3c00722.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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:oai:osti.gov:2202693","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2202693","pdf_url":null,"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},{"id":"pmh:oai:osti.gov:2229987","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/2229987","pdf_url":null,"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:escholarship.org:ark:/13030/qt77x0s1bx","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/77x0s1bx","pdf_url":"https://escholarship.org/content/qt77x0s1bx/qt77x0s1bx.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, vol 63, iss 21","raw_type":"article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G2825169058","display_name":null,"funder_award_id":"TC02274","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G5816449448","display_name":null,"funder_award_id":"DE-AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5847286610","display_name":null,"funder_award_id":"DE- AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"},{"id":"https://openalex.org/G8374966015","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G991281326","display_name":null,"funder_award_id":"AC52-07NA27344","funder_id":"https://openalex.org/F4320338286","funder_display_name":"Lawrence Livermore National Laboratory"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387692774.pdf","grobid_xml":"https://content.openalex.org/works/W4387692774.grobid-xml"},"referenced_works_count":72,"referenced_works":["https://openalex.org/W1548178570","https://openalex.org/W1604281503","https://openalex.org/W1808513053","https://openalex.org/W1966454287","https://openalex.org/W1982390234","https://openalex.org/W1982842980","https://openalex.org/W1984994707","https://openalex.org/W1997238096","https://openalex.org/W2024527855","https://openalex.org/W2040595595","https://openalex.org/W2042806682","https://openalex.org/W2055362477","https://openalex.org/W2060495448","https://openalex.org/W2067455153","https://openalex.org/W2069840353","https://openalex.org/W2096729078","https://openalex.org/W2101223914","https://openalex.org/W2104295259","https://openalex.org/W2112878061","https://openalex.org/W2118190420","https://openalex.org/W2121688928","https://openalex.org/W2127322768","https://openalex.org/W2139932193","https://openalex.org/W2144528635","https://openalex.org/W2145578524","https://openalex.org/W2147627625","https://openalex.org/W2160642098","https://openalex.org/W2166765429","https://openalex.org/W2527836113","https://openalex.org/W2604527271","https://openalex.org/W2619948933","https://openalex.org/W2767891136","https://openalex.org/W2770630458","https://openalex.org/W2886036738","https://openalex.org/W2891992558","https://openalex.org/W2898397916","https://openalex.org/W2902128418","https://openalex.org/W2905356589","https://openalex.org/W2906083215","https://openalex.org/W2909200248","https://openalex.org/W2911658570","https://openalex.org/W2918544128","https://openalex.org/W2947103054","https://openalex.org/W2972330325","https://openalex.org/W2980583144","https://openalex.org/W2989646388","https://openalex.org/W2990428318","https://openalex.org/W2991688251","https://openalex.org/W3006781192","https://openalex.org/W3016962540","https://openalex.org/W3047739104","https://openalex.org/W3094379592","https://openalex.org/W3104537585","https://openalex.org/W3135935512","https://openalex.org/W3168436232","https://openalex.org/W3177567251","https://openalex.org/W3177828909","https://openalex.org/W3185701646","https://openalex.org/W3206017014","https://openalex.org/W3208672593","https://openalex.org/W3210786279","https://openalex.org/W4200060626","https://openalex.org/W4211238337","https://openalex.org/W4220718175","https://openalex.org/W4285020367","https://openalex.org/W4289080025","https://openalex.org/W4304140872","https://openalex.org/W4307035489","https://openalex.org/W4310948626","https://openalex.org/W4311573042","https://openalex.org/W4313857648","https://openalex.org/W4389324774"],"related_works":["https://openalex.org/W2334906681","https://openalex.org/W1559108998","https://openalex.org/W4387033830","https://openalex.org/W2776879684","https://openalex.org/W3013529667","https://openalex.org/W2612329522","https://openalex.org/W2467739942","https://openalex.org/W2139779008","https://openalex.org/W1993046136","https://openalex.org/W2006718226"],"abstract_inverted_index":{"Protein-ligand":[0],"interactions":[1,15,28],"are":[2,16,29,82],"essential":[3],"to":[4,51,58,68,89],"drug":[5,8],"discovery":[6],"and":[7,45,57,97,141],"development":[9],"efforts.":[10],"Desirable":[11],"on-target":[12],"or":[13,123],"multitarget":[14],"the":[17,30,85,107,111,116,127,138,143],"first":[18,31],"step":[19,32],"in":[20,33],"finding":[21],"an":[22],"effective":[23],"therapeutic,":[24],"while":[25],"undesirable":[26],"off-target":[27],"assessing":[34],"safety.":[35],"In":[36],"this":[37,100,130],"work,":[38],"we":[39],"introduce":[40],"a":[41,63,103,135],"novel":[42,60],"ligand-based":[43],"featurization":[44,131],"mapping":[46],"of":[47,99,106,115,129,137,147],"human":[48,108,139],"protein":[49,55,72,80],"pockets":[50,81],"identify":[52,69],"closely":[53],"related":[54],"targets":[56],"project":[59],"drugs":[61],"into":[62],"hybrid":[64],"protein-ligand":[65],"feature":[66],"space":[67],"their":[70,90],"likely":[71],"interactions.":[73],"Using":[74],"structure-based":[75],"template":[76,93],"matches":[77],"from":[78],"PDB,":[79],"featured":[83],"by":[84,120,133],"ligands":[86],"that":[87],"bind":[88],"best":[91],"co-complex":[92],"matches.":[94],"The":[95],"simplicity":[96],"interpretability":[98],"approach":[101],"provide":[102],"granular":[104],"characterization":[105,119],"proteome":[109,140],"at":[110],"protein-pocket":[112],"level":[113],"instead":[114],"traditional":[117],"protein-level":[118],"family,":[121],"function,":[122],"pathway.":[124],"We":[125],"demonstrate":[126],"power":[128],"method":[132],"clustering":[134],"subset":[136],"evaluating":[142],"predicted":[144],"cluster":[145],"associations":[146],"over":[148],"7000":[149],"compounds.":[150]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
