{"id":"https://openalex.org/W2809216727","doi":"https://doi.org/10.1093/bioinformatics/btz111","title":"DeepAffinity: interpretable deep learning of compound\u2013protein affinity through unified recurrent and convolutional neural networks","display_name":"DeepAffinity: interpretable deep learning of compound\u2013protein affinity through unified recurrent and convolutional neural networks","publication_year":2019,"publication_date":"2019-02-15","ids":{"openalex":"https://openalex.org/W2809216727","doi":"https://doi.org/10.1093/bioinformatics/btz111","mag":"2809216727","pmid":"https://pubmed.ncbi.nlm.nih.gov/30768156"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz111","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz111","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1806.07537","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069807825","display_name":"Mostafa Karimi","orcid":"https://orcid.org/0000-0002-1459-6832"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mostafa Karimi","raw_affiliation_strings":["Department of Electrical and Computer Engineering , College Station, TX, USA","TEES\u2013AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station , TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering , College Station, TX, USA","institution_ids":[]},{"raw_affiliation_string":"TEES\u2013AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station , TX, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087166824","display_name":"Di Wu","orcid":"https://orcid.org/0000-0002-6818-1886"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Di Wu","raw_affiliation_strings":["Department of Electrical and Computer Engineering , College Station, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering , College Station, TX, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048522863","display_name":"Zhangyang Wang","orcid":"https://orcid.org/0000-0002-2050-5693"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhangyang Wang","raw_affiliation_strings":["Department of Computer Science and Engineering, Texas A&M University, College Station , TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Texas A&M University, College Station , TX, USA","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100716873","display_name":"Yang Shen","orcid":"https://orcid.org/0000-0002-1703-7796"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yang Shen","raw_affiliation_strings":["Department of Electrical and Computer Engineering , College Station, TX, USA","TEES\u2013AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station , TX, USA"],"raw_orcid":"https://orcid.org/0000-0002-1703-7796","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering , College Station, TX, USA","institution_ids":[]},{"raw_affiliation_string":"TEES\u2013AgriLife Center for Bioinformatics and Genomic Systems Engineering, College Station , TX, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100716873"],"corresponding_institution_ids":[],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":38.1678,"has_fulltext":false,"cited_by_count":553,"citation_normalized_percentile":{"value":0.99905516,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"35","issue":"18","first_page":"3329","last_page":"3338"},"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":0.9986000061035156,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9943000078201294,"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/interpretability","display_name":"Interpretability","score":0.944937527179718},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7387920022010803},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6739345788955688},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6579158306121826},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6175479888916016},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6015023589134216},{"id":"https://openalex.org/keywords/labeled-data","display_name":"Labeled data","score":0.5647333860397339},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49691274762153625},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.48299872875213623},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.4461904764175415},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4154196083545685},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3685801327228546},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21000272035598755},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16929465532302856},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1112094521522522}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.944937527179718},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7387920022010803},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6739345788955688},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6579158306121826},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6175479888916016},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6015023589134216},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.5647333860397339},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49691274762153625},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.48299872875213623},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.4461904764175415},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4154196083545685},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3685801327228546},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21000272035598755},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16929465532302856},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1112094521522522}],"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz111","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz111","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30768156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30768156","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":"Journal Article"},{"id":"pmh:oai:arXiv.org:1806.07537","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1806.07537","pdf_url":"https://arxiv.org/pdf/1806.07537","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6748780","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6748780","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1806.07537","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1806.07537","pdf_url":"https://arxiv.org/pdf/1806.07537","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G556791467","display_name":null,"funder_award_id":"R35 GM124952","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6538414090","display_name":"Unraveling molecular and system-level mechanisms of human disease-associated protein mutations","funder_award_id":"2r35gm124952-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G706427378","display_name":null,"funder_award_id":"FA8750-18-2-0027","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320334350","display_name":"High Performance Research Computing, Texas A and M University","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W104184427","https://openalex.org/W141181845","https://openalex.org/W1614298861","https://openalex.org/W1722029454","https://openalex.org/W1753482797","https://openalex.org/W1950993160","https://openalex.org/W1964069747","https://openalex.org/W1975147762","https://openalex.org/W2012438480","https://openalex.org/W2018796817","https://openalex.org/W2019974881","https://openalex.org/W2021348977","https://openalex.org/W2044002635","https://openalex.org/W2096495474","https://openalex.org/W2096864392","https://openalex.org/W2101279411","https://openalex.org/W2102461176","https://openalex.org/W2117620409","https://openalex.org/W2126671570","https://openalex.org/W2127553917","https://openalex.org/W2131347449","https://openalex.org/W2131474431","https://openalex.org/W2138512826","https://openalex.org/W2147152072","https://openalex.org/W2147526198","https://openalex.org/W2189911347","https://openalex.org/W2214665483","https://openalex.org/W2259538443","https://openalex.org/W2282821441","https://openalex.org/W2342838938","https://openalex.org/W2399976582","https://openalex.org/W2407258532","https://openalex.org/W2471196942","https://openalex.org/W2556131117","https://openalex.org/W2558217333","https://openalex.org/W2604306554","https://openalex.org/W2606780347","https://openalex.org/W2735246657","https://openalex.org/W2741292700","https://openalex.org/W2753953057","https://openalex.org/W2771472444","https://openalex.org/W2784213390","https://openalex.org/W2786722833","https://openalex.org/W2791366550","https://openalex.org/W2807792492","https://openalex.org/W2949504121","https://openalex.org/W2949888546","https://openalex.org/W2950577311","https://openalex.org/W2963102887","https://openalex.org/W2963819570","https://openalex.org/W2964199361","https://openalex.org/W2964347220","https://openalex.org/W4240895940","https://openalex.org/W4295547865","https://openalex.org/W6636510571","https://openalex.org/W6688357764","https://openalex.org/W6730280152","https://openalex.org/W6735840763","https://openalex.org/W6736685754","https://openalex.org/W6747927160","https://openalex.org/W6748947987"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W4390569940","https://openalex.org/W2888392564","https://openalex.org/W4361193272","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W2768320620","https://openalex.org/W3193920202","https://openalex.org/W4318813552","https://openalex.org/W2576964996"],"abstract_inverted_index":{"MOTIVATION:":[0],"Drug":[1],"discovery":[2],"demands":[3],"rapid":[4],"quantification":[5],"of":[6,15,37,46],"compound-protein":[7,20],"interaction":[8],"(CPI).":[9],"However,":[10],"there":[11],"is":[12],"a":[13,34,51,163],"lack":[14],"methods":[16],"that":[17,56],"can":[18],"predict":[19],"affinity":[21],"from":[22],"sequences":[23,158],"alone":[24],"with":[25,113],"high":[26],"applicability,":[27],"accuracy":[28],"and":[29,40,59,70,78,83,99,125,131,148,162,183],"interpretability.":[30],"RESULTS:":[31],"We":[32],"present":[33],"seamless":[35],"integration":[36],"domain":[38],"knowledges":[39],"learning-based":[41],"approaches.":[42],"Under":[43],"novel":[44],"representations":[45,77,82,155],"structurally":[47],"annotated":[48],"protein":[49,102,111,157],"sequences,":[50],"semi-supervised":[52],"deep":[53],"learning":[54],"model":[55,135,166],"unifies":[57],"recurrent":[58],"convolutional":[60],"neural":[61],"networks":[62],"has":[63],"been":[64],"proposed":[65],"to":[66,133,136,138,174],"exploit":[67],"both":[68],"unlabeled":[69],"labeled":[71,115],"data,":[72],"for":[73,96,101,106,109,146],"jointly":[74],"encoding":[75],"molecular":[76],"predicting":[79,147],"affinities.":[80],"Our":[81],"models":[84],"outperform":[85],"conventional":[86],"options":[87],"in":[88,92,143],"achieving":[89],"relative":[90],"error":[91],"IC50":[93],"within":[94],"5-fold":[95],"test":[97],"cases":[98],"20-fold":[100],"classes":[103,112],"not":[104],"included":[105],"training.":[107],"Performances":[108],"new":[110],"few":[114],"data":[116,193],"are":[117,129,171,186,194],"further":[118],"improved":[119],"by":[120],"transfer":[121],"learning.":[122],"Furthermore,":[123],"separate":[124],"joint":[126],"attention":[127],"mechanisms":[128],"developed":[130],"embedded":[132],"our":[134],"add":[137],"its":[139],"interpretability,":[140],"as":[141],"illustrated":[142],"case":[144],"studies":[145],"explaining":[149],"selective":[150],"drug-target":[151],"interactions.":[152],"Lastly,":[153],"alternative":[154],"using":[156,167],"or":[159],"compound":[160],"graphs":[161],"unified":[164],"RNN/GCNN-CNN":[165],"graph":[168],"CNN":[169],"(GCNN)":[170],"also":[172],"explored":[173],"reveal":[175],"algorithmic":[176],"challenges":[177],"ahead.":[178],"AVAILABILITY":[179],"AND":[180],"IMPLEMENTATION:":[181],"Data":[182],"source":[184],"codes":[185],"available":[187,195],"at":[188,196],"https://github.com/Shen-Lab/DeepAffinity.":[189],"SUPPLEMENTARY":[190],"INFORMATION:":[191],"Supplementary":[192],"Bioinformatics":[197],"online.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":47},{"year":2025,"cited_by_count":88},{"year":2024,"cited_by_count":103},{"year":2023,"cited_by_count":105},{"year":2022,"cited_by_count":91},{"year":2021,"cited_by_count":69},{"year":2020,"cited_by_count":37},{"year":2019,"cited_by_count":12}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}