{"id":"https://openalex.org/W4282827695","doi":"https://doi.org/10.1093/bib/bbac231","title":"Multiphysical graph neural network (MP-GNN) for COVID-19 drug design","display_name":"Multiphysical graph neural network (MP-GNN) for COVID-19 drug design","publication_year":2022,"publication_date":"2022-06-13","ids":{"openalex":"https://openalex.org/W4282827695","doi":"https://doi.org/10.1093/bib/bbac231","pmid":"https://pubmed.ncbi.nlm.nih.gov/35696650"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac231","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/A5100777893","display_name":"Xiaoshuang Li","orcid":"https://orcid.org/0000-0002-0773-6462"},"institutions":[{"id":"https://openalex.org/I45928872","display_name":"Alibaba Group (China)","ror":"https://ror.org/00k642b80","country_code":"CN","type":"company","lineage":["https://openalex.org/I45928872"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao-Shuang Li","raw_affiliation_strings":["Department of Computer Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University , China , 200240","Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University , China , 200240","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100408571","display_name":"Xiang Liu","orcid":"https://orcid.org/0000-0001-6046-1405"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Xiang Liu","raw_affiliation_strings":["Chern Institute of Mathematics and LPMC, Nankai University , Tianjin, China , 300071","Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371"],"affiliations":[{"raw_affiliation_string":"Chern Institute of Mathematics and LPMC, Nankai University , Tianjin, China , 300071","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045227579","display_name":"Le L\u00fc","orcid":"https://orcid.org/0000-0002-6799-9416"},"institutions":[{"id":"https://openalex.org/I45928872","display_name":"Alibaba Group (China)","ror":"https://ror.org/00k642b80","country_code":"CN","type":"company","lineage":["https://openalex.org/I45928872"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Lu","raw_affiliation_strings":["Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000"],"affiliations":[{"raw_affiliation_string":"Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024965898","display_name":"Xian\u2010Sheng Hua","orcid":"https://orcid.org/0000-0002-8232-5049"},"institutions":[{"id":"https://openalex.org/I45928872","display_name":"Alibaba Group (China)","ror":"https://ror.org/00k642b80","country_code":"CN","type":"company","lineage":["https://openalex.org/I45928872"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xian-Sheng Hua","raw_affiliation_strings":["Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000"],"affiliations":[{"raw_affiliation_string":"Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101793087","display_name":"Ying Chi","orcid":"https://orcid.org/0000-0002-3020-7892"},"institutions":[{"id":"https://openalex.org/I45928872","display_name":"Alibaba Group (China)","ror":"https://ror.org/00k642b80","country_code":"CN","type":"company","lineage":["https://openalex.org/I45928872"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Chi","raw_affiliation_strings":["Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000"],"affiliations":[{"raw_affiliation_string":"Healthcare Intelligence, AI Center, Alibaba Group DAMO Academy , China , 310000","institution_ids":["https://openalex.org/I45928872"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084610901","display_name":"Kelin Xia","orcid":"https://orcid.org/0000-0003-4183-0943"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Kelin Xia","raw_affiliation_strings":["Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371"],"affiliations":[{"raw_affiliation_string":"Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5084610901"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":8.5665,"has_fulltext":false,"cited_by_count":60,"citation_normalized_percentile":{"value":0.98263445,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"23","issue":"4","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":0.9980000257492065,"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":0.9894000291824341,"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":0.6634519696235657},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6158631443977356},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.504158616065979},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44487541913986206},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32360947132110596},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32229992747306824}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6634519696235657},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6158631443977356},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.504158616065979},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44487541913986206},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32360947132110596},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32229992747306824},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000093485","descriptor_name":"COVID-19 Drug Treatment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000093485","descriptor_name":"COVID-19 Drug Treatment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000093485","descriptor_name":"COVID-19 Drug Treatment","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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac231","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:35696650","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35696650","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":[{"id":"https://metadata.un.org/sdg/3","score":0.7200000286102295,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1681224145","https://openalex.org/W2046589863","https://openalex.org/W2114162221","https://openalex.org/W2290847742","https://openalex.org/W2343550476","https://openalex.org/W2526925775","https://openalex.org/W2610142609","https://openalex.org/W2733638363","https://openalex.org/W2741292700","https://openalex.org/W2753588101","https://openalex.org/W2789758093","https://openalex.org/W2801991413","https://openalex.org/W2860192827","https://openalex.org/W2895884529","https://openalex.org/W2913099012","https://openalex.org/W2951676304","https://openalex.org/W2963121255","https://openalex.org/W2963646740","https://openalex.org/W2963833291","https://openalex.org/W2963883198","https://openalex.org/W2963969719","https://openalex.org/W2969457089","https://openalex.org/W2984249386","https://openalex.org/W3001282080","https://openalex.org/W3007309629","https://openalex.org/W3014346445","https://openalex.org/W3014881833","https://openalex.org/W3032123378","https://openalex.org/W3082498841","https://openalex.org/W3089819726","https://openalex.org/W3096561213","https://openalex.org/W3100157108","https://openalex.org/W3158144848","https://openalex.org/W3161138623","https://openalex.org/W3167575787","https://openalex.org/W4236965008","https://openalex.org/W4249970808","https://openalex.org/W4287554881","https://openalex.org/W4295547865","https://openalex.org/W6735840763","https://openalex.org/W6739778489","https://openalex.org/W6748328607","https://openalex.org/W6768286814","https://openalex.org/W6772311615","https://openalex.org/W6775123410","https://openalex.org/W6786774367"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W2087343574","https://openalex.org/W2121910908"],"abstract_inverted_index":{"Graph":[0],"neural":[1,37,311],"networks":[2],"(GNNs)":[3],"are":[4,64,87,96,143,156,187],"the":[5,43,171,207,220,293,300],"most":[6],"promising":[7],"deep":[8],"learning":[9,117],"models":[10,86,100,239],"that":[11,284],"can":[12,235,315],"revolutionize":[13],"non-Euclidean":[14],"data":[15,321],"analysis.":[16],"However,":[17],"their":[18,274],"full":[19],"potential":[20,295,303],"is":[21,168,202,248,287],"severely":[22],"curtailed":[23],"by":[24,67,146,158],"poorly":[25],"represented":[26,66,157],"molecular":[27,46,54,135],"graphs":[28,74,162],"and":[29,49,60,72,107,114,231],"features.":[30,78,197],"Here,":[31],"we":[32,243,272],"propose":[33],"a":[34,68,159,210,258],"multiphysical":[35,45],"graph":[36,47,82,149,191,310],"network":[38,84,312],"(MP-GNN)":[39,313],"model":[40,234,314],"based":[41],"on":[42,219,257],"developed":[44],"representation":[48],"featurization.":[50],"All":[51],"kinds":[52],"of":[53,70,161,263,288,296,302],"interactions,":[55],"between":[56],"different":[57,62,102,105,141,164],"atom":[58,185],"types":[59],"at":[61,104,163],"scales,":[63,106],"systematically":[65],"series":[69,160],"scale-specific":[71],"element-specific":[73,190],"with":[75,89,193,260],"distance-related":[76,195],"node":[77,196],"From":[79],"these":[80],"graphs,":[81],"convolution":[83],"(GCN)":[85],"constructed":[88,97],"specially":[90],"designed":[91,203],"weight-sharing":[92],"architectures.":[93],"Base":[94],"learners":[95],"from":[98,101,139,170,226],"GCN":[99],"elements":[103],"further":[108],"consolidated":[109,211],"together":[110],"using":[111,131,277],"both":[112],"one-scale":[113],"multi-scale":[115],"ensemble":[116],"schemes.":[118],"Our":[119,213,233],"MP-GNN":[120,127,214,247,286,298],"has":[121,215,281],"two":[122],"distinct":[123],"properties.":[124],"First,":[125],"our":[126,182,246,278,285,297],"incorporates":[128],"multiscale":[129],"interactions":[130,138,186],"more":[132],"than":[133],"one":[134,147],"graph.":[136],"Atomic":[137],"various":[140,184],"scales":[142],"not":[144],"modeled":[145],"specific":[148],"(as":[150],"in":[151,177,250,318],"traditional":[152],"GNNs),":[153],"instead":[154],"they":[155],"scales.":[165],"Second,":[166],"it":[167],"free":[169],"complicated":[172],"feature":[173],"generation":[174],"process":[175],"as":[176,240,242],"conventional":[178],"GNN":[179,200],"methods.":[180],"In":[181],"MP-GNN,":[183],"embedded":[188],"into":[189,209],"representations":[192],"only":[194],"A":[198],"unique":[199],"architecture":[201],"to":[204],"incorporate":[205],"all":[206,237],"information":[208],"model.":[212],"been":[216,282],"extensively":[217],"validated":[218],"widely":[221],"used":[222,249],"benchmark":[223],"test":[224],"datasets":[225],"PDBbind,":[227],"including":[228],"PDBbind-v2007,":[229],"PDBbind-v2013":[230],"PDBbind-v2016.":[232],"outperform":[236],"existing":[238],"far":[241],"know.":[244],"Further,":[245],"coronavirus":[251,270],"disease":[252],"2019":[253],"drug":[254],"design.":[255],"Based":[256],"dataset":[259],"185":[261],"complexes":[262],"inhibitors":[264],"for":[265,299,305],"severe":[266],"acute":[267],"respiratory":[268],"syndrome":[269],"(SARS-CoV/SARS-CoV-2),":[271],"evaluate":[273],"binding":[275],"affinities":[276],"MP-GNN.":[279],"It":[280],"found":[283,317],"high":[289],"accuracy.":[290],"This":[291],"demonstrates":[292],"great":[294],"screening":[301],"drugs":[304],"SARS-CoV-2.":[306],"Availability:":[307],"The":[308],"Multiphysical":[309],"be":[316,325],"https://github.com/Alibaba-DAMO-DrugAI/MGNN.":[319],"Additional":[320],"or":[322],"code":[323],"will":[324],"available":[326],"upon":[327],"reasonable":[328],"request.":[329]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}