{"id":"https://openalex.org/W4412454168","doi":"https://doi.org/10.1093/bioinformatics/btaf183","title":"Top-DTI: integrating topological deep learning and large language models for drug\u2013target interaction prediction","display_name":"Top-DTI: integrating topological deep learning and large language models for drug\u2013target interaction prediction","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454168","doi":"https://doi.org/10.1093/bioinformatics/btaf183","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662785"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf183","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i133/63745334/btaf183.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/Supplement_1/i133/63745334/btaf183.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061557341","display_name":"Muhammed Talo","orcid":"https://orcid.org/0000-0002-1595-5681"},"institutions":[{"id":"https://openalex.org/I123534392","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02","country_code":"US","type":"education","lineage":["https://openalex.org/I123534392"]},{"id":"https://openalex.org/I4210154513","display_name":"Sunny BioDiscovery (United States)","ror":"https://ror.org/04x5cyt12","country_code":"US","type":"company","lineage":["https://openalex.org/I4210154513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Muhammed Talo","raw_affiliation_strings":["BioDiscovery Institute, University of North Texas , Denton, TX 76207,","Center for Computational Life Sciences, University of North Texas , Denton, TX 76207,","Department of Computer Science and Engineering, University of North Texas , Denton 76207, TX,"],"affiliations":[{"raw_affiliation_string":"BioDiscovery Institute, University of North Texas , Denton, TX 76207,","institution_ids":["https://openalex.org/I123534392","https://openalex.org/I4210154513"]},{"raw_affiliation_string":"Center for Computational Life Sciences, University of North Texas , Denton, TX 76207,","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of North Texas , Denton 76207, TX,","institution_ids":["https://openalex.org/I123534392"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072283349","display_name":"Serdar Bozdag","orcid":"https://orcid.org/0000-0002-4813-4310"},"institutions":[{"id":"https://openalex.org/I123534392","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02","country_code":"US","type":"education","lineage":["https://openalex.org/I123534392"]},{"id":"https://openalex.org/I4210154513","display_name":"Sunny BioDiscovery (United States)","ror":"https://ror.org/04x5cyt12","country_code":"US","type":"company","lineage":["https://openalex.org/I4210154513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Serdar Bozdag","raw_affiliation_strings":["BioDiscovery Institute, University of North Texas , Denton, TX 76207,","Center for Computational Life Sciences, University of North Texas , Denton, TX 76207,","Department of Computer Science and Engineering, University of North Texas , Denton 76207, TX,","Department of Mathematics, University of North Texas , Denton, TX 76207,"],"affiliations":[{"raw_affiliation_string":"BioDiscovery Institute, University of North Texas , Denton, TX 76207,","institution_ids":["https://openalex.org/I123534392","https://openalex.org/I4210154513"]},{"raw_affiliation_string":"Center for Computational Life Sciences, University of North Texas , Denton, TX 76207,","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of North Texas , Denton 76207, TX,","institution_ids":["https://openalex.org/I123534392"]},{"raw_affiliation_string":"Department of Mathematics, University of North Texas , Denton, TX 76207,","institution_ids":["https://openalex.org/I123534392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5061557341"],"corresponding_institution_ids":["https://openalex.org/I123534392","https://openalex.org/I4210154513"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8264,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.916188,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i133","last_page":"i141"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9951000213623047,"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":0.9951000213623047,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9904000163078308,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9528999924659729,"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/robustness","display_name":"Robustness (evolution)","score":0.7319166660308838},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7266160249710083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6211296319961548},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5424663424491882},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4249376654624939},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4124448895454407},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33456695079803467},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09888583421707153}],"concepts":[{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7319166660308838},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7266160249710083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6211296319961548},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5424663424491882},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4249376654624939},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4124448895454407},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33456695079803467},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09888583421707153},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","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":"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":"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":"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":"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":"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":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf183","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i133/63745334/btaf183.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:40662785","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662785","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:12261471","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261471","pdf_url":null,"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","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/btaf183","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf183","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i133/63745334/btaf183.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":[{"id":"https://openalex.org/G1141759092","display_name":null,"funder_award_id":"R35GM133657","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8135516887","display_name":null,"funder_award_id":"R35GM133657","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310911","display_name":"University of North Texas","ror":"https://ror.org/00v97ad02"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454168.pdf","grobid_xml":"https://content.openalex.org/works/W4412454168.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W2087726892","https://openalex.org/W2106887764","https://openalex.org/W2148145769","https://openalex.org/W2153838454","https://openalex.org/W2785947426","https://openalex.org/W2899788782","https://openalex.org/W3015234645","https://openalex.org/W3018980093","https://openalex.org/W3028589594","https://openalex.org/W3038922487","https://openalex.org/W3093397714","https://openalex.org/W3096561213","https://openalex.org/W3111174583","https://openalex.org/W3122066254","https://openalex.org/W3177500196","https://openalex.org/W3187980261","https://openalex.org/W3206585172","https://openalex.org/W4292265045","https://openalex.org/W4294558607","https://openalex.org/W4307178567","https://openalex.org/W4308565024","https://openalex.org/W4313485929","https://openalex.org/W4318981550","https://openalex.org/W4367048244","https://openalex.org/W4379932151","https://openalex.org/W4387874094","https://openalex.org/W4390971145","https://openalex.org/W4391444806","https://openalex.org/W4391824669","https://openalex.org/W4392298624","https://openalex.org/W4392458883","https://openalex.org/W4401532898","https://openalex.org/W4404572688","https://openalex.org/W6681677808","https://openalex.org/W6738964360","https://openalex.org/W6846383865","https://openalex.org/W6861883798"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W4321353415","https://openalex.org/W2745001401","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W4246352526","https://openalex.org/W2121910908","https://openalex.org/W915438175","https://openalex.org/W4230315250"],"abstract_inverted_index":{"The":[0],"data":[1],"and":[2],"source":[3],"code":[4],"of":[5],"Top-DTI":[6],"are":[7],"available":[8],"at":[9],"https://github.com/bozdaglab/Top_DTI":[10],"under":[11],"the":[12],"Creative":[13],"Commons":[14],"Attribution":[15],"NonCommercial":[16],"4.0":[17],"International":[18],"Public":[19],"License.":[20]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
