{"id":"https://openalex.org/W4206488367","doi":"https://doi.org/10.1109/bibm52615.2021.9669781","title":"Structure-Based Protein-Drug Affinity Prediction with Spatial Attention Mechanisms","display_name":"Structure-Based Protein-Drug Affinity Prediction with Spatial Attention Mechanisms","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4206488367","doi":"https://doi.org/10.1109/bibm52615.2021.9669781"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669781","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100721973","display_name":"Yuxiao Wang","orcid":"https://orcid.org/0000-0002-4162-4587"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxiao Wang","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041699085","display_name":"Zongzhao Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zongzhao Qiu","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010616947","display_name":"Qihong Jiao","orcid":null},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qihong Jiao","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420548","display_name":"Cheng Chen","orcid":"https://orcid.org/0000-0002-4203-2145"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Chen","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073704794","display_name":"Zhaoxu Meng","orcid":"https://orcid.org/0000-0003-0686-0231"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoxu Meng","raw_affiliation_strings":["Shandong University,School of Life Sciences,Qingdao,China","School of Life Sciences, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Life Sciences,Qingdao,China","institution_ids":["https://openalex.org/I154099455"]},{"raw_affiliation_string":"School of Life Sciences, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.6038,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.95847751,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"92","last_page":"97"},"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":0.9961000084877014,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9891999959945679,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6940528154373169},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6727502942085266},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6245659589767456},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5942445397377014},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.56163090467453},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5138407349586487},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.5038389563560486},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.4904596507549286},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.48542794585227966},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4538693130016327},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.44724974036216736},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4455069303512573},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4345102906227112},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18711453676223755},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.13664942979812622},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09160387516021729}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6940528154373169},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6727502942085266},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6245659589767456},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5942445397377014},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.56163090467453},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5138407349586487},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.5038389563560486},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.4904596507549286},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.48542794585227966},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4538693130016327},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.44724974036216736},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4455069303512573},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4345102906227112},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18711453676223755},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.13664942979812622},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09160387516021729},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.0},{"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669781","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1993046136","https://openalex.org/W1993403967","https://openalex.org/W2013085020","https://openalex.org/W2049185580","https://openalex.org/W2105668062","https://openalex.org/W2108243628","https://openalex.org/W2112796928","https://openalex.org/W2121972740","https://openalex.org/W2148512505","https://openalex.org/W2152630148","https://openalex.org/W2279098554","https://openalex.org/W2296686360","https://openalex.org/W2617750324","https://openalex.org/W2741292700","https://openalex.org/W2781821160","https://openalex.org/W2784213390","https://openalex.org/W2884585870","https://openalex.org/W2889677957","https://openalex.org/W2899663614","https://openalex.org/W2902812092","https://openalex.org/W2945755098","https://openalex.org/W2951676304","https://openalex.org/W2963969719","https://openalex.org/W3004617930","https://openalex.org/W3005043246","https://openalex.org/W3044938537","https://openalex.org/W3099810371","https://openalex.org/W3127104022","https://openalex.org/W3135935512","https://openalex.org/W3178461144","https://openalex.org/W6695314431","https://openalex.org/W6753412334","https://openalex.org/W6755977528"],"related_works":["https://openalex.org/W4241081643","https://openalex.org/W1974414168","https://openalex.org/W1971291106","https://openalex.org/W1996889227","https://openalex.org/W2924053807","https://openalex.org/W2769641421","https://openalex.org/W2120642597","https://openalex.org/W2337206335","https://openalex.org/W2484487206","https://openalex.org/W2952522307"],"abstract_inverted_index":{"Discovery":[0],"of":[1,11,22,177,188,202,219],"new":[2],"drugs":[3],"heavily":[4],"relies":[5],"on":[6,65,141,209,225],"predicting":[7],"the":[8,44,48,125,142,171,178,191,210,216],"binding":[9,103,160,180],"affinities":[10,181],"drug":[12,16,33],"molecules":[13],"to":[14,29,52,86,118,205],"suitable":[15],"targets.":[17],"To":[18],"accelerate":[19],"this":[20],"process":[21],"identifying":[23],"accurate":[24,75],"affinities,":[25],"computer-aided":[26],"methods":[27,39,51],"need":[28],"be":[30,99,134],"applied":[31],"in":[32,43,129],"discovery":[34],"pipeline.":[35],"While":[36],"various":[37],"computational":[38],"have":[40],"been":[41],"developed":[42],"past":[45],"ten":[46],"years,":[47],"most":[49],"successful":[50],"date":[53],"use":[54],"3D":[55],"convolutional":[56],"neural":[57],"networks":[58,62],"(3D-CNNs).":[59],"These":[60],"3D-CNN":[61,111],"are":[63,70,157],"based":[64],"deep":[66],"learning":[67,78],"models,":[68],"and":[69,73,89,190,227],"both":[71],"faster":[72],"more":[74,140],"than":[76],"machine":[77],"methods.":[79],"However,":[80],"currently":[81,206],"used":[82,207],"CNN":[83],"is":[84,222],"difficult":[85],"learn":[87],"global":[88],"spatial":[90,113,120],"features,":[91],"while":[92],"we":[93,107,165],"hypothesis":[94,153],"that":[95,136,154,167],"spacial":[96,127,155],"features":[97,156],"should":[98],"critical":[100,158],"for":[101,159],"structure-based":[102],"affinity":[104,161],"predictions.":[105,162],"Here":[106],"propose":[108],"an":[109,185,199],"end-to-end":[110],"with":[112],"attention":[114],"mechanisms,":[115],"called":[116],"saCNN,":[117],"encourage":[119],"feature":[121],"learning.":[122],"When":[123],"visualizing":[124],"learned":[126],"attentions":[128],"our":[130,152,168,220],"experiments,":[131],"it":[132],"can":[133],"observed":[135],"saCNN":[137],"model":[138,169,221],"focuses":[139],"voxels":[143],"near":[144],"interaction":[145],"centers.":[146],"This":[147],"key":[148],"observation":[149],"well":[150],"supports":[151],"In":[163],"additions,":[164],"show":[166],"improves":[170],"Root":[172],"Mean":[173],"Square":[174],"Error":[175],"(RMSE)":[176],"predicted":[179],"by":[182,196],"11.5%":[183],"(with":[184,198],"absolute":[186,200],"value":[187,201],"1.117)":[189],"Pearson":[192],"Correlation":[193],"Coefficient":[194],"(R)":[195],"3.2%":[197],"0.865)":[203],"compared":[204],"models":[208],"PDBbind":[211],"v.2016":[212],"core":[213],"set.":[214],"Importantly,":[215],"generalization":[217],"abilities":[218],"further":[223],"demonstrated":[224],"CASF-2013":[226],"CASF-2007":[228],"datasets.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4}],"updated_date":"2026-07-04T06:09:54.619538","created_date":"2025-10-10T00:00:00"}
