{"id":"https://openalex.org/W4414785070","doi":"https://doi.org/10.1021/acs.jcim.5c01974","title":"ML-PLA: Enhancing Protein\u2013Ligand Binding Affinity Prediction with Microenvironment and Long-Range Interaction-Aware Graph Neural Networks","display_name":"ML-PLA: Enhancing Protein\u2013Ligand Binding Affinity Prediction with Microenvironment and Long-Range Interaction-Aware Graph Neural Networks","publication_year":2025,"publication_date":"2025-10-03","ids":{"openalex":"https://openalex.org/W4414785070","doi":"https://doi.org/10.1021/acs.jcim.5c01974","pmid":"https://pubmed.ncbi.nlm.nih.gov/41042215"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c01974","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01974","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5006543131","display_name":"Yajie Meng","orcid":"https://orcid.org/0000-0002-2384-1158"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yajie Meng","raw_affiliation_strings":["School of Computer Science and Artificial Intelligence","Wuhan Textile University","School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence","institution_ids":[]},{"raw_affiliation_string":"Wuhan Textile University","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100632245","display_name":"Zhuang Zhang","orcid":"https://orcid.org/0000-0002-9496-2934"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuang Zhang","raw_affiliation_strings":["Hainan University","School of Computer Science and Artificial Intelligence","School of Computer Science and Technology","Wuhan Textile University","School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hainan University","institution_ids":["https://openalex.org/I20942203"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Wuhan Textile University","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052987594","display_name":"Jincan Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jincan Li","raw_affiliation_strings":["School of Computer Science and Artificial Intelligence","Wuhan Textile University","School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence","institution_ids":[]},{"raw_affiliation_string":"Wuhan Textile University","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016425036","display_name":"Xianfang Tang","orcid":"https://orcid.org/0000-0002-6895-2898"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianfang Tang","raw_affiliation_strings":["School of Computer Science and Artificial Intelligence","Wuhan Textile University","School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence","institution_ids":[]},{"raw_affiliation_string":"Wuhan Textile University","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei 430200, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065538319","display_name":"Changcheng Lu","orcid":"https://orcid.org/0000-0001-9263-8463"},"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":"Changcheng Lu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering","Hunan University","College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering","institution_ids":[]},{"raw_affiliation_string":"Hunan University","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan 410082, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353028","display_name":"Zilong Zhang","orcid":"https://orcid.org/0000-0002-4934-1258"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilong Zhang","raw_affiliation_strings":["Hainan University","School of Computer Science and Artificial Intelligence","School of Computer Science and Technology","Wuhan Textile University"],"raw_orcid":"https://orcid.org/0000-0002-4934-1258","affiliations":[{"raw_affiliation_string":"Hainan University","institution_ids":["https://openalex.org/I20942203"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Wuhan Textile University","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061028143","display_name":"Feifei Cui","orcid":"https://orcid.org/0000-0001-7055-3813"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feifei Cui","raw_affiliation_strings":["Hainan University","School of Computer Science and Technology","School of Computer Science and Technology, Hainan University, Haikou, Hainan 570228, China"],"raw_orcid":"https://orcid.org/0000-0001-7055-3813","affiliations":[{"raw_affiliation_string":"Hainan University","institution_ids":["https://openalex.org/I20942203"]},{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, Hainan 570228, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055170451","display_name":"Pan Zeng","orcid":"https://orcid.org/0000-0002-6674-9749"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pan Zeng","raw_affiliation_strings":["Chongqing Normal University","School of Computer and Information Science","School of Computer and Information Science, Chongqing Normal University, Chongqing 401331, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chongqing Normal University","institution_ids":["https://openalex.org/I126924076"]},{"raw_affiliation_string":"School of Computer and Information Science","institution_ids":[]},{"raw_affiliation_string":"School of Computer and Information Science, Chongqing Normal University, Chongqing 401331, China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343678","display_name":"Bo Li","orcid":"https://orcid.org/0000-0001-5760-5682"},"institutions":[{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]},{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Li","raw_affiliation_strings":["School of Computer Science and Technology","Wuhan University of Science and Technology","School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei 430065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Wuhan University of Science and Technology","institution_ids":["https://openalex.org/I43922553"]},{"raw_affiliation_string":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei 430065, China","institution_ids":["https://openalex.org/I43922553"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066469263","display_name":"Junlin Xu","orcid":"https://orcid.org/0000-0003-1057-1504"},"institutions":[{"id":"https://openalex.org/I4390039265","display_name":"PRG S&Tech (South Korea)","ror":"https://ror.org/02sr2ee22","country_code":null,"type":"company","lineage":["https://openalex.org/I4390039265"]},{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junlin Xu","raw_affiliation_strings":["School of Computer Science and Technology","Wuhan University of Science and Technology"],"raw_orcid":"https://orcid.org/0000-0003-1057-1504","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology","institution_ids":["https://openalex.org/I4390039265"]},{"raw_affiliation_string":"Wuhan University of Science and Technology","institution_ids":["https://openalex.org/I43922553"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5066469263"],"corresponding_institution_ids":["https://openalex.org/I4390039265","https://openalex.org/I43922553"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.27655832,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"20","first_page":"10988","last_page":"10998"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"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":0.9997000098228455,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9977999925613403,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9965999722480774,"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/exploit","display_name":"Exploit","score":0.6172999739646912},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5497000217437744},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.54339998960495},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5113000273704529},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.5008000135421753},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4909999966621399},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.3871000111103058},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.38100001215934753}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7049999833106995},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.6172999739646912},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5497000217437744},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.54339998960495},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5113000273704529},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.5008000135421753},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4909999966621399},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4523000121116638},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.43560001254081726},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3871000111103058},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.38100001215934753},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.35440000891685486},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32199999690055847},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3091000020503998},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.29350000619888306},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2903999984264374},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2802000045776367},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2775000035762787},{"id":"https://openalex.org/C53052385","wikidata":"https://www.wikidata.org/wiki/Q17104046","display_name":"Mixed graph","level":5,"score":0.2745000123977661},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2694999873638153},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2639999985694885},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.26010000705718994},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.258899986743927},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.2542000114917755}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c01974","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c01974","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41042215","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41042215","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3060302192","display_name":null,"funder_award_id":"62402349","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3742730607","display_name":null,"funder_award_id":"2024AFB127","funder_id":"https://openalex.org/F4320322186","funder_display_name":"Natural Science Foundation of Hubei Province"},{"id":"https://openalex.org/G5355520699","display_name":null,"funder_award_id":"2023JJ40180","funder_id":"https://openalex.org/F4320322843","funder_display_name":"Natural Science Foundation of\u00a0Hunan Province"},{"id":"https://openalex.org/G5901061461","display_name":null,"funder_award_id":"2024309","funder_id":"https://openalex.org/F4320327462","funder_display_name":"Wuhan Textile University"},{"id":"https://openalex.org/G6063895130","display_name":null,"funder_award_id":"20230612","funder_id":"https://openalex.org/F4320327462","funder_display_name":"Wuhan Textile University"},{"id":"https://openalex.org/G8235456468","display_name":null,"funder_award_id":"62302156","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/F4320322186","display_name":"Natural Science Foundation of Hubei Province","ror":null},{"id":"https://openalex.org/F4320322843","display_name":"Natural Science Foundation of\u00a0Hunan Province","ror":null},{"id":"https://openalex.org/F4320327462","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1993046136","https://openalex.org/W2013085020","https://openalex.org/W2076779488","https://openalex.org/W2550887636","https://openalex.org/W2612690371","https://openalex.org/W2781821160","https://openalex.org/W2784213390","https://openalex.org/W2785947426","https://openalex.org/W2902812092","https://openalex.org/W2963833291","https://openalex.org/W2965857891","https://openalex.org/W2968734407","https://openalex.org/W2969996838","https://openalex.org/W2974531988","https://openalex.org/W2990138404","https://openalex.org/W3001433048","https://openalex.org/W3015208165","https://openalex.org/W3022395336","https://openalex.org/W3098189759","https://openalex.org/W3151148247","https://openalex.org/W3167575787","https://openalex.org/W3204651332","https://openalex.org/W3212042276","https://openalex.org/W4200139236","https://openalex.org/W4280538744","https://openalex.org/W4281381643","https://openalex.org/W4282917061","https://openalex.org/W4290876361","https://openalex.org/W4317776906","https://openalex.org/W4321004126","https://openalex.org/W4324129409","https://openalex.org/W4377968189","https://openalex.org/W4380739447","https://openalex.org/W4382318714","https://openalex.org/W4385763856","https://openalex.org/W4388627827","https://openalex.org/W4389836921","https://openalex.org/W4391560080","https://openalex.org/W4392454655","https://openalex.org/W4392500218","https://openalex.org/W4400879287","https://openalex.org/W4407212030"],"related_works":[],"abstract_inverted_index":{"Accurately":[0],"predicting":[1],"protein-ligand":[2,152],"binding":[3],"affinity":[4],"(PLA)":[5],"is":[6],"essential":[7],"in":[8],"drug":[9],"discovery":[10],"for":[11],"identifying":[12],"lead":[13],"compounds.":[14],"The":[15],"sequence":[16,53,117],"and":[17,32,54,118,135,196,205],"structural":[18,55],"contexts":[19],"of":[20,52,137,170,209],"an":[21],"amino":[22],"acid":[23],"residue":[24],"(i.e.,":[25],"microenvironment)":[26],"describe":[27],"the":[28,66,83,133,168,179,183,194,202],"surrounding":[29],"chemical":[30],"properties":[31],"geometric":[33],"features.":[34],"While":[35],"recent":[36],"graph-based":[37],"models":[38],"have":[39],"shown":[40],"considerable":[41],"promise,":[42],"they":[43],"often":[44],"construct":[45],"microenvironment":[46],"representations":[47],"using":[48,159],"a":[49,70,97,105,127,160],"shallow":[50],"fusion":[51],"features,":[56],"potentially":[57],"failing":[58],"to":[59,74,85,110,131],"capture":[60,132],"their":[61],"full":[62],"synergistic":[63],"effects.":[64],"Furthermore,":[65,124],"common":[67],"reliance":[68],"on":[69,193],"fixed":[71],"distance":[72],"threshold":[73],"define":[75],"interaction":[76,148,180],"space,":[77],"while":[78,187],"computationally":[79],"efficient,":[80],"inherently":[81],"limits":[82],"ability":[84],"model":[86,111],"key":[87],"nonlocal":[88],"biological":[89],"phenomena.":[90],"To":[91,144],"address":[92],"these":[93],"issues,":[94],"we":[95,125],"propose":[96],"novel":[98],"method":[99],"named":[100],"ML-PLA.":[101],"Specifically,":[102],"ML-PLA":[103,150,210],"employs":[104],"heterogeneous":[106],"graph":[107,171],"neural":[108,172],"network":[109,173],"protein":[112],"microenvironments":[113],"by":[114],"aggregating":[115],"both":[116],"structure":[119],"information":[120,181],"from":[121],"neighboring":[122],"nodes.":[123],"incorporate":[126],"vector":[128],"quantized-variational":[129],"autoencoder":[130],"diversity":[134],"complexity":[136],"microenvironments,":[138],"producing":[139],"chemically":[140],"meaningful,":[141],"fine-grained":[142],"representations.":[143],"effectively":[145,177],"exploit":[146],"long-range":[147],"information,":[149],"projects":[151],"complex":[153,184],"atoms":[154,158],"into":[155,182],"multiple":[156],"virtual":[157],"multihead":[161],"attention":[162],"mechanism,":[163],"rather":[164],"than":[165],"simply":[166],"increasing":[167],"number":[169],"layers.":[174],"This":[175],"approach":[176],"embeds":[178],"atom":[185],"features":[186],"simultaneously":[188],"avoiding":[189],"oversmoothing.":[190],"Extensive":[191],"experiments":[192],"CASF-2016":[195],"CASF-2013":[197],"benchmark":[198],"data":[199],"sets":[200],"demonstrate":[201],"significant":[203],"effectiveness":[204],"robust":[206],"generalization":[207],"capabilities":[208],"compared":[211],"with":[212],"state-of-the-art":[213],"methods.":[214]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
