{"id":"https://openalex.org/W3167283626","doi":"https://doi.org/10.1109/jbhi.2021.3089162","title":"3DMol-Net: Learn 3D Molecular Representation Using Adaptive Graph Convolutional Network Based on Rotation Invariance","display_name":"3DMol-Net: Learn 3D Molecular Representation Using Adaptive Graph Convolutional Network Based on Rotation Invariance","publication_year":2021,"publication_date":"2021-06-14","ids":{"openalex":"https://openalex.org/W3167283626","doi":"https://doi.org/10.1109/jbhi.2021.3089162","mag":"3167283626","pmid":"https://pubmed.ncbi.nlm.nih.gov/34125693"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2021.3089162","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3089162","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100409235","display_name":"Chunyan Li","orcid":"https://orcid.org/0000-0003-3014-3363"},"institutions":[{"id":"https://openalex.org/I145897649","display_name":"Minzu University of China","ror":"https://ror.org/0044e2g62","country_code":"CN","type":"education","lineage":["https://openalex.org/I145897649"]},{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chunyan Li","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, China","Yunnan Minzu University, Kunming, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Yunnan Minzu University, Kunming, China","institution_ids":["https://openalex.org/I145897649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100323752","display_name":"Wei Wei","orcid":"https://orcid.org/0000-0002-7566-2995"},"institutions":[{"id":"https://openalex.org/I110440473","display_name":"Xi'an University of Science and Technology","ror":"https://ror.org/046fkpt18","country_code":"CN","type":"education","lineage":["https://openalex.org/I110440473"]},{"id":"https://openalex.org/I4210131919","display_name":"Xi'an University of Technology","ror":"https://ror.org/038avdt50","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210131919"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Wei","raw_affiliation_strings":["School of Computer Science and Engineering, Xian University of Technology, Xian, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Xian University of Technology, Xian, China","institution_ids":["https://openalex.org/I110440473","https://openalex.org/I4210131919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100364789","display_name":"Jin Li","orcid":"https://orcid.org/0000-0002-3628-7037"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Li","raw_affiliation_strings":["School of Software, Yunnan University, Kunming, China"],"affiliations":[{"raw_affiliation_string":"School of Software, Yunnan University, Kunming, China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051198154","display_name":"Junfeng Yao","orcid":"https://orcid.org/0000-0002-2330-7406"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Yao","raw_affiliation_strings":["School of Informatics, Xiamen University, Xiamen, China"],"affiliations":[{"raw_affiliation_string":"School of Informatics, Xiamen University, Xiamen, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027286013","display_name":"Xiangxiang Zeng","orcid":"https://orcid.org/0000-0001-6201-0114"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108044017","display_name":"Zhihan Lv","orcid":"https://orcid.org/0009-0005-9452-5768"},"institutions":[{"id":"https://openalex.org/I108688024","display_name":"Qingdao University","ror":"https://ror.org/021cj6z65","country_code":"CN","type":"education","lineage":["https://openalex.org/I108688024"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihan Lv","raw_affiliation_strings":["School of Data Science and Software Engineering, Qingdao University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"School of Data Science and Software Engineering, Qingdao University, Qingdao, China","institution_ids":["https://openalex.org/I108688024"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100409235"],"corresponding_institution_ids":["https://openalex.org/I145897649","https://openalex.org/I191208505"],"apc_list":null,"apc_paid":null,"fwci":4.391,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.94860903,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"26","issue":"10","first_page":"5044","last_page":"5054"},"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":0.9973000288009644,"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":0.984499990940094,"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":0.6871822476387024},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.6264846324920654},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5873672366142273},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5818913578987122},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.556415319442749},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.542595624923706},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5318151712417603},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.47315678000450134},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4521503746509552},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44268354773521423},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.40029966831207275},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18772485852241516},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.0942811369895935}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6871822476387024},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.6264846324920654},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5873672366142273},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5818913578987122},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.556415319442749},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.542595624923706},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5318151712417603},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.47315678000450134},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4521503746509552},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44268354773521423},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.40029966831207275},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18772485852241516},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0942811369895935},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"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":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012399","descriptor_name":"Rotation","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},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2021.3089162","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2021.3089162","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:34125693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34125693","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6600000262260437}],"awards":[{"id":"https://openalex.org/G383104888","display_name":null,"funder_award_id":"62072388","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5528392975","display_name":null,"funder_award_id":"2020J0362","funder_id":"https://openalex.org/F4320324734","funder_display_name":"Yunnan Provincial Department of Education"},{"id":"https://openalex.org/G5801954405","display_name":null,"funder_award_id":"61902203","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"},{"id":"https://openalex.org/F4320324734","display_name":"Yunnan Provincial Department of Education","ror":"https://ror.org/02yrxdp92"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1738019091","https://openalex.org/W1975997599","https://openalex.org/W1976848779","https://openalex.org/W1988037271","https://openalex.org/W1991252559","https://openalex.org/W2010700988","https://openalex.org/W2024046085","https://openalex.org/W2030971064","https://openalex.org/W2076498053","https://openalex.org/W2158787690","https://openalex.org/W2214665483","https://openalex.org/W2290847742","https://openalex.org/W2461470610","https://openalex.org/W2583907533","https://openalex.org/W2594183968","https://openalex.org/W2726670313","https://openalex.org/W2734982589","https://openalex.org/W2799307902","https://openalex.org/W2901003004","https://openalex.org/W2904859708","https://openalex.org/W2918239264","https://openalex.org/W2946099214","https://openalex.org/W2950128007","https://openalex.org/W2951048875","https://openalex.org/W2963017945","https://openalex.org/W2964015378","https://openalex.org/W2966357564","https://openalex.org/W2969996838","https://openalex.org/W2970472075","https://openalex.org/W2984339599","https://openalex.org/W2992752586","https://openalex.org/W3020930839","https://openalex.org/W3034516664","https://openalex.org/W3035547893","https://openalex.org/W3041085747","https://openalex.org/W3098465726","https://openalex.org/W3100157108","https://openalex.org/W3111918841","https://openalex.org/W3143789190","https://openalex.org/W3145734614","https://openalex.org/W3155577228","https://openalex.org/W4289674602","https://openalex.org/W6631190155","https://openalex.org/W6637178625","https://openalex.org/W6637865168","https://openalex.org/W6685350579","https://openalex.org/W6688357764","https://openalex.org/W6697873463","https://openalex.org/W6713134421","https://openalex.org/W6720006811","https://openalex.org/W6726873649","https://openalex.org/W6736685754","https://openalex.org/W6753859757","https://openalex.org/W6756302984","https://openalex.org/W6757146439","https://openalex.org/W6793761863","https://openalex.org/W6966986580"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W4293226380","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2156434174","https://openalex.org/W2013842271","https://openalex.org/W2808877228"],"abstract_inverted_index":{"Studying":[0],"the":[1,14,35,50,73,76,79,83,98,104,117,122,129,144,148],"deep":[2],"learning-based":[3],"molecular":[4,11,45,107,118,131,137,168],"representation":[5,201],"has":[6],"great":[7],"significance":[8],"on":[9,91],"predicting":[10],"property,":[12],"promoted":[13],"development":[15],"of":[16,37,54,69,75,82,106,128,147,155,184,192,203],"drug":[17,21,38,77],"screening":[18],"and":[19,23,63,78,124,159,170,187,194,200],"new":[20],"discovery,":[22],"improving":[24],"human":[25],"well-being":[26],"for":[27,39],"avoiding":[28],"illnesses.":[29],"It":[30],"is":[31],"essential":[32],"to":[33,115,143,151,166],"learn":[34,152],"characterization":[36],"various":[40],"downstream":[41],"tasks,":[42],"such":[43],"as":[44],"property":[46],"prediction.":[47,65],"In":[48,109],"particular,":[49],"3D":[51,67,99,130,149,153],"structure":[52,158],"features":[53],"molecules":[55,70],"play":[56],"an":[57,161],"important":[58],"role":[59],"in":[60,182],"biochemical":[61,171],"function":[62],"activity":[64],"The":[66],"characteristics":[68,81],"largely":[71],"determine":[72],"properties":[74,95,169],"binding":[80],"target.":[84],"However,":[85],"most":[86],"current":[87,175],"methods":[88],"merely":[89],"rely":[90],"1D":[92],"or":[93],"2D":[94],"while":[96],"ignoring":[97],"topological":[100],"structure,":[101],"thereby":[102],"degrading":[103],"performance":[105,181],"inferring.":[108],"this":[110],"paper,":[111],"we":[112,134],"propose":[113],"3DMol-Net":[114,178],"enhance":[116],"representation,":[119],"considering":[120],"both":[121,185],"topology":[123,154],"rotation":[125],"invariance":[126],"(RI)":[127],"structure.":[132],"Specifically,":[133],"construct":[135],"a":[136],"graph":[138,157,163],"with":[139,174],"soft":[140],"relations":[141],"related":[142],"spatial":[145],"arrangement":[146],"coordinates":[150],"arbitrary":[156],"employ":[160],"adaptive":[162],"convolutional":[164],"network":[165],"predict":[167],"activities.":[172],"Comparing":[173],"graph-based":[176],"methods,":[177],"demonstrates":[179],"superior":[180],"terms":[183],"regression":[186],"classification":[188],"tasks.":[189],"Further":[190],"verification":[191],"RI":[193],"visualization":[195],"also":[196],"show":[197],"better":[198],"robustness":[199],"capacity":[202],"our":[204],"model.":[205]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
