{"id":"https://openalex.org/W3020511336","doi":"https://doi.org/10.1021/acs.jcim.0c00026","title":"Binding Affinity Prediction by Pairwise Function Based on Neural Network","display_name":"Binding Affinity Prediction by Pairwise Function Based on Neural Network","publication_year":2020,"publication_date":"2020-04-27","ids":{"openalex":"https://openalex.org/W3020511336","doi":"https://doi.org/10.1021/acs.jcim.0c00026","mag":"3020511336","pmid":"https://pubmed.ncbi.nlm.nih.gov/32338892"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00026","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00026","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":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/1756151","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079002066","display_name":"Fangqiang Zhu","orcid":"https://orcid.org/0000-0001-6202-2262"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fangqiang Zhu","raw_affiliation_strings":["Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States"],"affiliations":[{"raw_affiliation_string":"Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100439355","display_name":"Xiaohua Zhang","orcid":"https://orcid.org/0000-0003-0102-6352"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohua Zhang","raw_affiliation_strings":["Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States"],"affiliations":[{"raw_affiliation_string":"Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035849909","display_name":"Jonathan Allen","orcid":"https://orcid.org/0000-0002-4359-8263"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan E. Allen","raw_affiliation_strings":["Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States"],"affiliations":[{"raw_affiliation_string":"Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020229955","display_name":"Derek Jones","orcid":"https://orcid.org/0000-0002-9510-6662"},"institutions":[{"id":"https://openalex.org/I4210138311","display_name":"Lawrence Livermore National Security","ror":"https://ror.org/03z21mf61","country_code":"US","type":"government","lineage":["https://openalex.org/I4210138311"]},{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Derek Jones","raw_affiliation_strings":["Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States"],"affiliations":[{"raw_affiliation_string":"Global Security, Computing Applications Division, Computing Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I4210138311","https://openalex.org/I1282311441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020056606","display_name":"Felice C. Lightstone","orcid":"https://orcid.org/0000-0003-1465-426X"},"institutions":[{"id":"https://openalex.org/I1282311441","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282311441","https://openalex.org/I1330989302","https://openalex.org/I198811213","https://openalex.org/I4210138311"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Felice C. Lightstone","raw_affiliation_strings":["Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States"],"affiliations":[{"raw_affiliation_string":"Biochemical and Biophysical Systems Group, Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States","institution_ids":["https://openalex.org/I1282311441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5079002066"],"corresponding_institution_ids":["https://openalex.org/I1282311441"],"apc_list":null,"apc_paid":null,"fwci":7.0751,"has_fulltext":false,"cited_by_count":71,"citation_normalized_percentile":{"value":0.97539561,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"60","issue":"6","first_page":"2766","last_page":"2772"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9980000257492065,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9843999743461609,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.8517662286758423},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5763109922409058},{"id":"https://openalex.org/keywords/logarithm","display_name":"Logarithm","score":0.5014059543609619},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.4960664212703705},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.48377057909965515},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48160049319267273},{"id":"https://openalex.org/keywords/dissociation-constant","display_name":"Dissociation constant","score":0.4745003879070282},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4427618980407715},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.376523494720459},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3204955756664276},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.284050315618515},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09104049205780029},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07082474231719971}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.8517662286758423},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5763109922409058},{"id":"https://openalex.org/C39927690","wikidata":"https://www.wikidata.org/wiki/Q11197","display_name":"Logarithm","level":2,"score":0.5014059543609619},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.4960664212703705},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.48377057909965515},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48160049319267273},{"id":"https://openalex.org/C74998103","wikidata":"https://www.wikidata.org/wiki/Q898254","display_name":"Dissociation constant","level":3,"score":0.4745003879070282},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4427618980407715},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.376523494720459},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3204955756664276},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.284050315618515},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09104049205780029},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07082474231719971},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"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":"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":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c00026","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00026","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:32338892","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32338892","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},{"id":"pmh:oai:osti.gov:1756151","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1756151","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1756151","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1756151","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8999999761581421}],"awards":[{"id":"https://openalex.org/G2825169058","display_name":null,"funder_award_id":"TC02274","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"}],"funders":[{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1526205344","https://openalex.org/W1984476711","https://openalex.org/W1986853728","https://openalex.org/W1988037271","https://openalex.org/W1993403967","https://openalex.org/W2050273205","https://openalex.org/W2050456292","https://openalex.org/W2072683434","https://openalex.org/W2073021822","https://openalex.org/W2089188080","https://openalex.org/W2092285329","https://openalex.org/W2115256962","https://openalex.org/W2118233996","https://openalex.org/W2121621209","https://openalex.org/W2134967712","https://openalex.org/W2147993766","https://openalex.org/W2151919617","https://openalex.org/W2154670681","https://openalex.org/W2158360182","https://openalex.org/W2334483166","https://openalex.org/W2404280981","https://openalex.org/W2550887636","https://openalex.org/W2583907533","https://openalex.org/W2587598315","https://openalex.org/W2730519791","https://openalex.org/W2895884529","https://openalex.org/W2902812092","https://openalex.org/W2918239264","https://openalex.org/W3104705366","https://openalex.org/W4234276140"],"related_works":["https://openalex.org/W1523821527","https://openalex.org/W2571978672","https://openalex.org/W2007257620","https://openalex.org/W1914280947","https://openalex.org/W1594539819","https://openalex.org/W4213038553","https://openalex.org/W2413373620","https://openalex.org/W3037560061","https://openalex.org/W2511693580","https://openalex.org/W2058674645"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,55,59,81],"new":[3],"approach":[4],"to":[5,109,125,129],"estimate":[6],"the":[7,37,43,46,64,67,84,104],"binding":[8,39],"affinity":[9,95],"from":[10],"given":[11],"three-dimensional":[12],"poses":[13],"of":[14,31,45,66,83,116],"protein-ligand":[15,21],"complexes.":[16],"In":[17],"this":[18],"scheme,":[19],"every":[20],"atom":[22],"pair":[23],"makes":[24],"an":[25],"additive":[26],"free-energy":[27],"contribution.":[28],"The":[29,49,75,89,119],"sum":[30],"these":[32],"pairwise":[33,50,76],"contributions":[34],"then":[35],"gives":[36],"total":[38],"free":[40],"energy":[41],"or":[42],"logarithm":[44],"dissociation":[47],"constant.":[48],"contribution":[51],"is":[52,78],"calculated":[53],"by":[54],"function":[56,77],"implemented":[57],"via":[58],"neural":[60],"network":[61],"that":[62,115],"takes":[63],"properties":[65],"two":[68],"atoms":[69],"and":[70,102,134],"their":[71],"distance":[72],"as":[73,114],"input.":[74],"trained":[79],"using":[80],"portion":[82],"PDBbind":[85,100],"2018":[86,101],"data":[87],"set.":[88],"model":[90],"achieves":[91],"good":[92],"accuracy":[93,133],"for":[94],"predictions":[96],"when":[97],"evaluated":[98],"with":[99,103],"CASF-2016":[105],"benchmark,":[106],"comparing":[107],"favorably":[108],"many":[110],"scoring":[111],"functions":[112],"such":[113],"AutoDock":[117],"Vina.":[118],"framework":[120],"here":[121],"may":[122],"be":[123],"extended":[124],"incorporate":[126],"other":[127],"factors":[128],"further":[130],"improve":[131],"its":[132],"power.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
