{"id":"https://openalex.org/W4390605827","doi":"https://doi.org/10.1021/acs.jcim.3c01170","title":"A High-Quality Data Set of Protein\u2013Ligand Binding Interactions Via Comparative Complex Structure Modeling","display_name":"A High-Quality Data Set of Protein\u2013Ligand Binding Interactions Via Comparative Complex Structure Modeling","publication_year":2024,"publication_date":"2024-01-05","ids":{"openalex":"https://openalex.org/W4390605827","doi":"https://doi.org/10.1021/acs.jcim.3c01170","pmid":"https://pubmed.ncbi.nlm.nih.gov/38181418"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01170","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01170","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/A5068505823","display_name":"Xuelian Li","orcid":"https://orcid.org/0000-0002-4063-3043"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuelian Li","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]},{"raw_affiliation_string":"National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China","institution_ids":["https://openalex.org/I200296433"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102000226","display_name":"Cheng Shen","orcid":"https://orcid.org/0000-0002-8888-3316"},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Shen","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040344252","display_name":"Hui Zhu","orcid":"https://orcid.org/0000-0002-4024-374X"},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Zhu","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]},{"raw_affiliation_string":"Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056838978","display_name":"Yujian Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yujian Yang","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048815132","display_name":"Qing Wang","orcid":"https://orcid.org/0000-0002-1155-2340"},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qing Wang","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044785440","display_name":"Jincai Yang","orcid":"https://orcid.org/0000-0002-0033-0187"},"institutions":[{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jincai Yang","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074665620","display_name":"Niu Huang","orcid":"https://orcid.org/0000-0002-6912-033X"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210086405","display_name":"National Institute of Biological Sciences, Beijing","ror":"https://ror.org/00wksha49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210086405"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Niu Huang","raw_affiliation_strings":["National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China","Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China"],"affiliations":[{"raw_affiliation_string":"National Institute of Biological Sciences, 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China","institution_ids":["https://openalex.org/I4210086405"]},{"raw_affiliation_string":"National Institute of Biological Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China","institution_ids":["https://openalex.org/I200296433"]},{"raw_affiliation_string":"Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5044785440","https://openalex.org/A5074665620"],"corresponding_institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210086405","https://openalex.org/I99065089"],"apc_list":null,"apc_paid":null,"fwci":6.8221,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.9727024,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"64","issue":"7","first_page":"2454","last_page":"2466"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5919821858406067},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.558109700679779},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.5528513789176941},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.5396682024002075},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5274391770362854},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5060111880302429},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45338308811187744},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.43145108222961426},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4207618236541748},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.38828137516975403},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3751259744167328},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36476099491119385},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35043787956237793},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.34292924404144287},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32558107376098633},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.21289095282554626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11593130230903625}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5919821858406067},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.558109700679779},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.5528513789176941},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.5396682024002075},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5274391770362854},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5060111880302429},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45338308811187744},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.43145108222961426},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4207618236541748},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.38828137516975403},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3751259744167328},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36476099491119385},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35043787956237793},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.34292924404144287},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32558107376098633},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.21289095282554626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11593130230903625},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","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/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"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":"D015195","descriptor_name":"Drug Design","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},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01170","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01170","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:38181418","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38181418","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":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.6000000238418579}],"awards":[{"id":"https://openalex.org/G7060692123","display_name":null,"funder_award_id":"Z201100005320012","funder_id":"https://openalex.org/F4320325902","funder_display_name":"Beijing Municipal Science and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320322392","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549"},{"id":"https://openalex.org/F4320325902","display_name":"Beijing Municipal Science and Technology Commission","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":93,"referenced_works":["https://openalex.org/W330953206","https://openalex.org/W1527782499","https://openalex.org/W1604884792","https://openalex.org/W1604972505","https://openalex.org/W2000350990","https://openalex.org/W2017254234","https://openalex.org/W2018661561","https://openalex.org/W2020372058","https://openalex.org/W2027376226","https://openalex.org/W2030971064","https://openalex.org/W2040990879","https://openalex.org/W2042694699","https://openalex.org/W2046639437","https://openalex.org/W2051594610","https://openalex.org/W2058311929","https://openalex.org/W2070880994","https://openalex.org/W2072683434","https://openalex.org/W2074978477","https://openalex.org/W2079096219","https://openalex.org/W2092285329","https://openalex.org/W2094162409","https://openalex.org/W2096864392","https://openalex.org/W2105391890","https://openalex.org/W2111078532","https://openalex.org/W2114520383","https://openalex.org/W2129153475","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2139362074","https://openalex.org/W2146465875","https://openalex.org/W2147988069","https://openalex.org/W2155142785","https://openalex.org/W2204695023","https://openalex.org/W2244785476","https://openalex.org/W2274656763","https://openalex.org/W2291647668","https://openalex.org/W2394923207","https://openalex.org/W2401258374","https://openalex.org/W2404280981","https://openalex.org/W2517767579","https://openalex.org/W2558366645","https://openalex.org/W2583907533","https://openalex.org/W2587598315","https://openalex.org/W2789748145","https://openalex.org/W2803615944","https://openalex.org/W2824810263","https://openalex.org/W2882976371","https://openalex.org/W2900090807","https://openalex.org/W2902812092","https://openalex.org/W2912171584","https://openalex.org/W2925328360","https://openalex.org/W2955986556","https://openalex.org/W2955998834","https://openalex.org/W2970175280","https://openalex.org/W2980863799","https://openalex.org/W3001433048","https://openalex.org/W3008726875","https://openalex.org/W3030018498","https://openalex.org/W3082411326","https://openalex.org/W3135935512","https://openalex.org/W3159719254","https://openalex.org/W3168436232","https://openalex.org/W3172303648","https://openalex.org/W3173174268","https://openalex.org/W3177828909","https://openalex.org/W3198923619","https://openalex.org/W3201597079","https://openalex.org/W3206116522","https://openalex.org/W3211414347","https://openalex.org/W3216686093","https://openalex.org/W4200509818","https://openalex.org/W4210307613","https://openalex.org/W4213370488","https://openalex.org/W4220823532","https://openalex.org/W4224936511","https://openalex.org/W4225286967","https://openalex.org/W4225896682","https://openalex.org/W4229060137","https://openalex.org/W4233606194","https://openalex.org/W4248107770","https://openalex.org/W4281381643","https://openalex.org/W4282913408","https://openalex.org/W4288419263","https://openalex.org/W4294740789","https://openalex.org/W4306986475","https://openalex.org/W4310603653","https://openalex.org/W4311612485","https://openalex.org/W4321173085","https://openalex.org/W4376131268","https://openalex.org/W4377982332","https://openalex.org/W4385664952","https://openalex.org/W4387357260","https://openalex.org/W4388627827"],"related_works":["https://openalex.org/W3185720802","https://openalex.org/W4232045916","https://openalex.org/W2072444571","https://openalex.org/W2009937564","https://openalex.org/W4318472429","https://openalex.org/W1973079533","https://openalex.org/W4206949911","https://openalex.org/W3171039768","https://openalex.org/W3016550772","https://openalex.org/W2593264178"],"abstract_inverted_index":{"High-quality":[0],"protein-ligand":[1,60,74,162],"complex":[2,27,52,61],"structures":[3,28,62],"provide":[4],"the":[5,9,16,33,46,108,124,141],"basis":[6],"for":[7,91,120,139],"understanding":[8],"nature":[10],"of":[11,81],"noncovalent":[12],"binding":[13,65,147,163],"interactions":[14],"at":[15,170],"atomic":[17],"level":[18],"and":[19,79,135,145,160,166],"enable":[20],"structure-based":[21],"drug":[22],"design.":[23],"However,":[24],"experimentally":[25],"determined":[26],"are":[29],"scarce":[30],"compared":[31],"with":[32,63],"vast":[34],"chemical":[35],"space.":[36],"In":[37],"this":[38,42],"study,":[39],"we":[40,117],"addressed":[41],"issue":[43],"by":[44,111],"constructing":[45,157],"BindingNet":[47,68,105,134,153],"data":[48,126,164],"set":[49,165],"via":[50],"comparative":[51],"structure":[53],"modeling,":[54],"which":[55],"contains":[56],"69,816":[57],"modeled":[58],"high-quality":[59],"experimental":[64],"affinity":[66],"data.":[67],"provides":[69],"valuable":[70],"insights":[71],"into":[72],"investigating":[73],"interactions,":[75],"allowing":[76],"visual":[77],"inspection":[78],"interpretation":[80],"structural":[82],"analogues'":[83],"structure-activity":[84],"relationships.":[85],"It":[86],"can":[87],"also":[88,129],"be":[89],"used":[90],"evaluating":[92],"machine-learning-based":[93],"scoring":[94],"functions.":[95],"Our":[96],"results":[97],"indicate":[98],"that":[99],"machine":[100],"learning":[101],"models":[102,121],"trained":[103,122],"on":[104,123],"could":[106],"reduce":[107],"bias":[109],"caused":[110],"buried":[112],"solvent-accessible":[113],"surface":[114],"area,":[115],"as":[116],"previously":[118],"found":[119],"PDBbind":[125,155],"set.":[127],"We":[128],"discussed":[130],"strategies":[131],"to":[132],"improve":[133],"its":[136],"potential":[137],"utilization":[138],"benchmarking":[140],"molecular":[142],"docking":[143],"methods":[144],"ligand":[146],"free":[148],"energy":[149],"calculation":[150],"approaches.":[151],"The":[152],"complements":[154],"in":[156],"a":[158],"sufficient":[159],"unbiased":[161],"is":[167],"freely":[168],"available":[169],"http://bindingnet.huanglab.org.cn.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
