{"id":"https://openalex.org/W4366991255","doi":"https://doi.org/10.1093/bib/bbad136","title":"BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing","display_name":"BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing","publication_year":2023,"publication_date":"2023-04-24","ids":{"openalex":"https://openalex.org/W4366991255","doi":"https://doi.org/10.1093/bib/bbad136","pmid":"https://pubmed.ncbi.nlm.nih.gov/37096593"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad136","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad136/50083388/bbad136.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad136/50083388/bbad136.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054474613","display_name":"Niloofar Yousefi","orcid":"https://orcid.org/0009-0005-0071-733X"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niloofar Yousefi","raw_affiliation_strings":["University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043368211","display_name":"Mehdi Yazdani-Jahromi","orcid":"https://orcid.org/0000-0001-6658-6591"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehdi Yazdani-Jahromi","raw_affiliation_strings":["University of Central Florida Computer Science, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida Computer Science, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024754640","display_name":"Aida Tayebi","orcid":null},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aida Tayebi","raw_affiliation_strings":["University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075351963","display_name":"Elayaraja Kolanthai","orcid":"https://orcid.org/0000-0003-2615-6866"},"institutions":[{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]},{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elayaraja Kolanthai","raw_affiliation_strings":["University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA","institution_ids":["https://openalex.org/I106165777","https://openalex.org/I94062374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013241705","display_name":"Craig J. Neal","orcid":"https://orcid.org/0000-0001-7288-4229"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Craig J Neal","raw_affiliation_strings":["University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA","institution_ids":["https://openalex.org/I106165777","https://openalex.org/I94062374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077764254","display_name":"Tanumoy Banerjee","orcid":"https://orcid.org/0000-0002-0862-6871"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tanumoy Banerjee","raw_affiliation_strings":["Lehigh University Department of Mechanical Engineering and Mechanics, , Bethlehem 18015, PA , USA"],"affiliations":[{"raw_affiliation_string":"Lehigh University Department of Mechanical Engineering and Mechanics, , Bethlehem 18015, PA , USA","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031686351","display_name":"Agnivo Gosai","orcid":"https://orcid.org/0000-0002-5146-509X"},"institutions":[{"id":"https://openalex.org/I1338503839","display_name":"Corning (United States)","ror":"https://ror.org/02tfv4t78","country_code":"US","type":"company","lineage":["https://openalex.org/I1338503839"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Agnivo Gosai","raw_affiliation_strings":["Independent Researcher , Corning, NY , USA"],"affiliations":[{"raw_affiliation_string":"Independent Researcher , Corning, NY , USA","institution_ids":["https://openalex.org/I1338503839"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072134023","display_name":"Ganesh Balasubramanian","orcid":"https://orcid.org/0000-0003-1834-5501"},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ganesh Balasubramanian","raw_affiliation_strings":["Lehigh University Department of Mechanical Engineering and Mechanics, , Bethlehem 18015, PA , USA"],"affiliations":[{"raw_affiliation_string":"Lehigh University Department of Mechanical Engineering and Mechanics, , Bethlehem 18015, PA , USA","institution_ids":["https://openalex.org/I186143895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026168431","display_name":"Sudipta Seal","orcid":"https://orcid.org/0000-0002-0963-3344"},"institutions":[{"id":"https://openalex.org/I4210145537","display_name":"Materials Processing (United States)","ror":"https://ror.org/05j00pb84","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145537"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]},{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sudipta Seal","raw_affiliation_strings":["University of Central Florida Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, , 4000 Central Florida Blvd., Orlando 32816, FL , USA","University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida Advanced Materials Processing and Analysis Center, Department of Materials Science and Engineering, , 4000 Central Florida Blvd., Orlando 32816, FL , USA","institution_ids":["https://openalex.org/I4210145537","https://openalex.org/I106165777"]},{"raw_affiliation_string":"University of Central Florida College of Medicine, Bionix Cluster, , 4000 Central Florida Blvd., Orlando 32816, FL , USA","institution_ids":["https://openalex.org/I106165777","https://openalex.org/I94062374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062903281","display_name":"\u00d6zlem \u00d6zmen Garibay","orcid":"https://orcid.org/0000-0001-9215-694X"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ozlem Ozmen Garibay","raw_affiliation_strings":["University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA"],"affiliations":[{"raw_affiliation_string":"University of Central Florida Industrial Engineering and Management Systems, , 32816, 4000 Central Florida Blvd., Orlando, FL , USA","institution_ids":["https://openalex.org/I106165777"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5062903281"],"corresponding_institution_ids":["https://openalex.org/I106165777"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":4.8064,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.95889454,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"24","issue":"3","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":1.0,"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":1.0,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9908000230789185,"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":0.7143661975860596},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.7045848965644836},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6392576098442078},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6116740107536316},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.564393937587738},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5532474517822266},{"id":"https://openalex.org/keywords/overfitting","display_name":"Overfitting","score":0.5202370882034302},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5177868604660034},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.5058426856994629},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49243173003196716},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.44988471269607544},{"id":"https://openalex.org/keywords/matthews-correlation-coefficient","display_name":"Matthews correlation coefficient","score":0.4154376685619354},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2020857036113739},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.198214590549469},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.14821156859397888},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12494918704032898},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10452982783317566}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7143661975860596},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7045848965644836},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6392576098442078},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6116740107536316},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.564393937587738},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5532474517822266},{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.5202370882034302},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5177868604660034},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.5058426856994629},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49243173003196716},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.44988471269607544},{"id":"https://openalex.org/C164085508","wikidata":"https://www.wikidata.org/wiki/Q4811327","display_name":"Matthews correlation coefficient","level":3,"score":0.4154376685619354},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2020857036113739},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.198214590549469},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.14821156859397888},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12494918704032898},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10452982783317566},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad136","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad136/50083388/bbad136.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37096593","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37096593","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10199763","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10199763","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10199763/pdf/bbad136.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad136","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad136","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad136/50083388/bbad136.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1631749026","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320310071","funder_display_name":"Indian Institute of Science"},{"id":"https://openalex.org/G1776607862","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306132","funder_display_name":"American Society for Engineering Education"}],"funders":[{"id":"https://openalex.org/F4320306132","display_name":"American Society for Engineering Education","ror":"https://ror.org/03ac64295"},{"id":"https://openalex.org/F4320310071","display_name":"Indian Institute of Science","ror":"https://ror.org/04dese585"},{"id":"https://openalex.org/F4320310161","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12"},{"id":"https://openalex.org/F4320338294","display_name":"Air Force Research Laboratory","ror":"https://ror.org/02e2egq70"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4366991255.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1972987731","https://openalex.org/W2003281617","https://openalex.org/W2011580004","https://openalex.org/W2012438480","https://openalex.org/W2023782921","https://openalex.org/W2035585923","https://openalex.org/W2044002635","https://openalex.org/W2086286404","https://openalex.org/W2109991441","https://openalex.org/W2138072853","https://openalex.org/W2138778824","https://openalex.org/W2145962544","https://openalex.org/W2399976582","https://openalex.org/W2407258532","https://openalex.org/W2529996553","https://openalex.org/W2605952223","https://openalex.org/W2744129621","https://openalex.org/W2754595644","https://openalex.org/W2785947426","https://openalex.org/W2793951981","https://openalex.org/W2798076125","https://openalex.org/W2806547269","https://openalex.org/W2807792492","https://openalex.org/W2809216727","https://openalex.org/W2899788782","https://openalex.org/W2911871527","https://openalex.org/W2918335507","https://openalex.org/W2989848927","https://openalex.org/W3004604833","https://openalex.org/W3005669732","https://openalex.org/W3007077815","https://openalex.org/W3012511738","https://openalex.org/W3014346445","https://openalex.org/W3032123378","https://openalex.org/W3088849005","https://openalex.org/W3096561213","https://openalex.org/W3098269892","https://openalex.org/W3164680581","https://openalex.org/W3197082762","https://openalex.org/W4244021009","https://openalex.org/W4285041843","https://openalex.org/W4292157312","https://openalex.org/W6653123006","https://openalex.org/W6695067062","https://openalex.org/W6736091738","https://openalex.org/W6752083957","https://openalex.org/W6775123410","https://openalex.org/W6800830003"],"related_works":["https://openalex.org/W2989932438","https://openalex.org/W4385957992","https://openalex.org/W4229079080","https://openalex.org/W2948863132","https://openalex.org/W4206534706","https://openalex.org/W3165136198","https://openalex.org/W3169068822","https://openalex.org/W4288336439","https://openalex.org/W4385965371","https://openalex.org/W4200511449"],"abstract_inverted_index":{"While":[0],"research":[1],"into":[2],"drug-target":[3,38],"interaction":[4,172],"(DTI)":[5],"prediction":[6,58,83,111,131,137,209,248],"is":[7,65,92],"fairly":[8],"mature,":[9],"generalizability":[10],"and":[11,61,99,158,198,232],"interpretability":[12],"are":[13],"not":[14],"always":[15],"addressed":[16],"in":[17,21,139,185,250],"the":[18,44,51,55,130,159,162,190,203,215,238,244],"existing":[19,88],"works":[20],"this":[22,25],"field.":[23],"In":[24],"paper,":[26],"we":[27,212],"propose":[28],"a":[29,105],"deep":[30],"learning":[31],"(DL)-based":[32],"framework,":[33],"called":[34],"BindingSite-AugmentedDTA,":[35],"which":[36,102,188],"improves":[37,81],"affinity":[39,57],"(DTA)":[40],"predictions":[41],"by":[42,113,174],"reducing":[43],"search":[45],"space":[46],"of":[47,50,108,133,141,181,218,240],"potential-binding":[48],"sites":[49],"protein,":[52],"thus":[53],"making":[54],"binding":[56,208,235],"more":[59],"efficient":[60],"accurate.":[62],"Our":[63],"BindingSite-AugmentedDTA":[64],"highly":[66,93],"generalizable":[67],"as":[68,200,202,243],"it":[69,79],"can":[70,103,128],"be":[71],"integrated":[72],"with":[73],"any":[74],"DL-based":[75],"regression":[76],"model,":[77],"while":[78],"significantly":[80],"their":[82],"performance.":[84],"Also,":[85],"unlike":[86],"many":[87],"models,":[89],"our":[90,126,219,241],"model":[91],"interpretable":[94],"due":[95],"to":[96,118,168],"its":[97,109],"architecture":[98],"self-attention":[100],"mechanism,":[101],"provide":[104],"deeper":[106],"understanding":[107],"underlying":[110],"mechanism":[112],"mapping":[114],"attention":[115],"weights":[116],"back":[117],"protein-binding":[119],"sites.":[120],"The":[121,225],"computational":[122],"results":[123],"confirm":[124],"that":[125],"framework":[127,221,242],"enhance":[129],"performance":[132],"seven":[134],"state-of-the-art":[135],"DTA":[136],"algorithms":[138],"terms":[140],"four":[142],"widely":[143],"used":[144,194],"evaluation":[145],"metrics,":[146],"including":[147,175],"concordance":[148],"index,":[149],"mean":[150],"squared":[151,154],"error,":[152],"modified":[153],"correlation":[155],"coefficient":[156],"($r^2_m$)":[157],"area":[160],"under":[161],"precision":[163],"curve.":[164],"We":[165],"also":[166],"contribute":[167],"three":[169],"benchmark":[170],"drug-traget":[171],"datasets":[173],"additional":[176],"information":[177],"on":[178],"3D":[179],"structure":[180],"all":[182],"proteins":[183],"contained":[184],"those":[186],"datasets,":[187,195],"include":[189],"two":[191],"most":[192],"commonly":[193],"namely":[196],"Kiba":[197],"Davis,":[199],"well":[201],"data":[204],"from":[205],"IDG-DREAM":[206],"drug-kinase":[207],"challenge.":[210],"Furthermore,":[211],"experimentally":[213,233],"validate":[214],"practical":[216],"potential":[217,239],"proposed":[220],"through":[222],"in-lab":[223],"experiments.":[224],"relatively":[226],"high":[227],"agreement":[228],"between":[229],"computationally":[230],"predicted":[231],"observed":[234],"interactions":[236],"supports":[237],"next-generation":[245],"pipeline":[246],"for":[247],"models":[249],"drug":[251],"repurposing.":[252]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
