{"id":"https://openalex.org/W4309452766","doi":"https://doi.org/10.1093/bib/bbac468","title":"Predicting drug\u2013target binding affinity through molecule representation block based on multi-head attention and skip connection","display_name":"Predicting drug\u2013target binding affinity through molecule representation block based on multi-head attention and skip connection","publication_year":2022,"publication_date":"2022-10-31","ids":{"openalex":"https://openalex.org/W4309452766","doi":"https://doi.org/10.1093/bib/bbac468","pmid":"https://pubmed.ncbi.nlm.nih.gov/36411674"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac468","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac468","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100425518","display_name":"Li Zhang","orcid":"https://orcid.org/0000-0002-1617-5943"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Zhang","raw_affiliation_strings":["School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027613930","display_name":"Chun-Chun Wang","orcid":"https://orcid.org/0000-0002-6795-4007"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun-Chun Wang","raw_affiliation_strings":["School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China"],"raw_orcid":"https://orcid.org/0000-0002-6795-4007","affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036210249","display_name":"Xing Chen","orcid":"https://orcid.org/0000-0001-9028-5342"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xing Chen","raw_affiliation_strings":["Artificial Intelligence Research Institute, China University of Mining and Technology , Xuzhou, 221116 , China","School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China"],"raw_orcid":"https://orcid.org/0000-0001-9028-5342","affiliations":[{"raw_affiliation_string":"Artificial Intelligence Research Institute, China University of Mining and Technology , Xuzhou, 221116 , China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou, 221116 , China","institution_ids":["https://openalex.org/I25757504"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5036210249"],"corresponding_institution_ids":["https://openalex.org/I25757504"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":17.0399,"has_fulltext":false,"cited_by_count":117,"citation_normalized_percentile":{"value":0.99485514,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"23","issue":"6","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/T10044","display_name":"Protein Structure and Dynamics","score":0.9940000176429749,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.979200005531311,"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":0.7599377036094666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6281964778900146},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.5776852369308472},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5138537883758545},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.511569082736969},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4306797385215759},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36269956827163696},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3478126525878906},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14269092679023743},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13262048363685608}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7599377036094666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6281964778900146},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.5776852369308472},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5138537883758545},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.511569082736969},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4306797385215759},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36269956827163696},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3478126525878906},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14269092679023743},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13262048363685608},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":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":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014481","descriptor_name":"United States","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac468","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac468","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36411674","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36411674","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G579333840","display_name":"\u57fa\u4e8e\u591a\u6e90\u6570\u636e\u878d\u5408\u7684\u836f\u7269\u54cd\u5e94\u548c\u836f\u7269\u76f8\u5173\u975e\u7f16\u7801RNA\u9776\u70b9\u9884\u6d4b\u7814\u7a76","funder_award_id":"61972399","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W1895993106","https://openalex.org/W1972987731","https://openalex.org/W2035585923","https://openalex.org/W2073414385","https://openalex.org/W2086286404","https://openalex.org/W2109991441","https://openalex.org/W2145962544","https://openalex.org/W2160931825","https://openalex.org/W2166550586","https://openalex.org/W2259538443","https://openalex.org/W2265264785","https://openalex.org/W2462108616","https://openalex.org/W2519887557","https://openalex.org/W2605952223","https://openalex.org/W2753953057","https://openalex.org/W2765950793","https://openalex.org/W2783536957","https://openalex.org/W2785947426","https://openalex.org/W2886544065","https://openalex.org/W2891279523","https://openalex.org/W2911871527","https://openalex.org/W2939293293","https://openalex.org/W2943974844","https://openalex.org/W2952992838","https://openalex.org/W2962711740","https://openalex.org/W2963579919","https://openalex.org/W2964015378","https://openalex.org/W2978036638","https://openalex.org/W2979463066","https://openalex.org/W2983936067","https://openalex.org/W2989611985","https://openalex.org/W2997234557","https://openalex.org/W2998571806","https://openalex.org/W3000043291","https://openalex.org/W3005064662","https://openalex.org/W3007309629","https://openalex.org/W3012012790","https://openalex.org/W3014346445","https://openalex.org/W3019745511","https://openalex.org/W3029836473","https://openalex.org/W3032908737","https://openalex.org/W3044927477","https://openalex.org/W3049770176","https://openalex.org/W3080123711","https://openalex.org/W3089819726","https://openalex.org/W3096561213","https://openalex.org/W3104744878","https://openalex.org/W3121015296","https://openalex.org/W3127145950","https://openalex.org/W3137359073","https://openalex.org/W3152586663","https://openalex.org/W3175798418","https://openalex.org/W3177525997","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3191666000","https://openalex.org/W3217681006","https://openalex.org/W4200233821","https://openalex.org/W4205167309","https://openalex.org/W4282827695","https://openalex.org/W4285723986","https://openalex.org/W4288262508","https://openalex.org/W4385245566","https://openalex.org/W6693339296","https://openalex.org/W6718962110","https://openalex.org/W6739901393","https://openalex.org/W6754929296","https://openalex.org/W6767235624","https://openalex.org/W6775123410","https://openalex.org/W6780226713","https://openalex.org/W6796707148"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W1986582023","https://openalex.org/W2966829450"],"abstract_inverted_index":{"Exiting":[0],"computational":[1],"models":[2,23],"for":[3,11,248],"drug-target":[4],"binding":[5,47,199,221],"affinity":[6],"prediction":[7,14,49,159],"have":[8],"much":[9],"room":[10],"improvement":[12],"in":[13,72,96,144,245],"accuracy,":[15],"robustness":[16],"and":[17,27,56,62,99,110,140,152,161,188,203,207,226],"generalization":[18],"ability.":[19],"Most":[20],"deep":[21],"learning":[22,64],"lack":[24],"interpretability":[25,173],"analysis":[26,174],"few":[28],"studies":[29,239],"provide":[30],"application":[31],"examples.":[32],"Based":[33],"on":[34,115,167],"these":[35],"observations,":[36],"we":[37,147,171,193,218],"presented":[38],"a":[39],"novel":[40],"model":[41],"named":[42],"Molecule":[43],"Representation":[44],"Block-based":[45],"Drug-Target":[46],"Affinity":[48],"(MRBDTA).":[50],"MRBDTA":[51,69,121,178,196,244],"is":[52],"composed":[53],"of":[54,68,87,163,183,237,243],"embedding":[55],"positional":[57],"encoding,":[58],"molecule":[59,81],"representation":[60],"block":[61,78,98,135,151],"interaction":[63,106,184],"module.":[65],"The":[66,112,234],"advantages":[67],"are":[70],"reflected":[71],"three":[73],"aspects:":[74],"(i)":[75],"developing":[76],"Trans":[77,97,134,138,145,150],"to":[79,104,175,197],"extract":[80],"features":[82],"through":[83,132],"improving":[84],"the":[85,102,123,158],"encoder":[86,94,139],"transformer,":[88],"(ii)":[89],"introducing":[90],"skip":[91,142,153],"connection":[92,143,154],"at":[93],"level":[95],"(iii)":[100],"enhancing":[101],"ability":[103],"capture":[105,181],"sites":[107,185],"between":[108,186,201,223],"proteins":[109,187],"drugs.":[111,189],"test":[113],"results":[114,236],"two":[116],"benchmark":[117],"datasets":[118],"manifest":[119],"that":[120,149,177],"achieves":[122],"best":[124],"performance":[125,242],"compared":[126,219],"with":[127,136,229],"11":[128],"state-of-the-art":[129],"models.":[130],"Besides,":[131],"replacing":[133],"single":[137],"removing":[141],"block,":[146],"verified":[148],"could":[155],"effectively":[156],"improve":[157],"accuracy":[160],"reliability":[162],"MRBDTA.":[164,233],"Then,":[165],"relying":[166],"multi-head":[168],"attention":[169],"mechanism,":[170],"performed":[172],"illustrate":[176],"can":[179],"correctly":[180],"part":[182],"In":[190],"case":[191,238],"studies,":[192],"firstly":[194],"employed":[195],"predict":[198],"affinities":[200,222],"Food":[202],"Drug":[204],"Administration-approved":[205],"drugs":[206,228],"severe":[208],"acute":[209],"respiratory":[210],"syndrome":[211],"coronavirus":[212],"2":[213],"(SARS-CoV-2)":[214],"replication-related":[215],"proteins.":[216],"Secondly,":[217],"true":[220],"3C-like":[224],"proteinase":[225],"185":[227],"those":[230],"predicted":[231],"by":[232],"final":[235],"reveal":[240],"reliable":[241],"drug":[246],"design":[247],"SARS-CoV-2.":[249]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":28},{"year":2024,"cited_by_count":53},{"year":2023,"cited_by_count":31}],"updated_date":"2026-06-12T08:23:45.883708","created_date":"2025-10-10T00:00:00"}
