{"id":"https://openalex.org/W2964549872","doi":"https://doi.org/10.1186/s13321-019-0373-4","title":"DLIGAND2: an improved knowledge-based energy function for protein\u2013ligand interactions using the distance-scaled, finite, ideal-gas reference state","display_name":"DLIGAND2: an improved knowledge-based energy function for protein\u2013ligand interactions using the distance-scaled, finite, ideal-gas reference state","publication_year":2019,"publication_date":"2019-08-07","ids":{"openalex":"https://openalex.org/W2964549872","doi":"https://doi.org/10.1186/s13321-019-0373-4","mag":"2964549872","pmid":"https://pubmed.ncbi.nlm.nih.gov/31392430"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-019-0373-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0373-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0373-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0373-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100642276","display_name":"Pin Chen","orcid":"https://orcid.org/0000-0001-8746-9917"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pin Chen","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0001-8746-9917","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069471124","display_name":"Yaobin Ke","orcid":"https://orcid.org/0000-0001-9575-5745"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaobin Ke","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0001-9575-5745","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101633465","display_name":"Yutong Lu","orcid":"https://orcid.org/0000-0001-5315-3375"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yutong Lu","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0001-5315-3375","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069366771","display_name":"Yunfei Du","orcid":"https://orcid.org/0000-0001-6832-0519"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunfei Du","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0001-6832-0519","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100462960","display_name":"Jiahui Li","orcid":"https://orcid.org/0000-0002-5455-9374"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahui Li","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0002-5455-9374","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102816713","display_name":"Yan Hui","orcid":"https://orcid.org/0000-0001-6653-1451"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Yan","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0001-6653-1451","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029051152","display_name":"Huiying Zhao","orcid":"https://orcid.org/0000-0001-9134-536X"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210097354","display_name":"Sun Yat-sen Memorial Hospital","ror":"https://ror.org/01px77p81","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210097354"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huiying Zhao","raw_affiliation_strings":["Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China. zhaohy8@mail.sysu.edu.cn","Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China"],"raw_orcid":"https://orcid.org/0000-0001-9134-536X","affiliations":[{"raw_affiliation_string":"Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China. zhaohy8@mail.sysu.edu.cn","institution_ids":["https://openalex.org/I4210097354","https://openalex.org/I157773358"]},{"raw_affiliation_string":"Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China","institution_ids":["https://openalex.org/I4210097354","https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032724151","display_name":"Yaoqi Zhou","orcid":"https://orcid.org/0000-0002-9958-5699"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Yaoqi Zhou","raw_affiliation_strings":["Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, 4215, Australia. yaoqi.zhou@griffith.edu.au","Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, 4215, Australia"],"raw_orcid":"https://orcid.org/0000-0002-9958-5699","affiliations":[{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, 4215, Australia. yaoqi.zhou@griffith.edu.au","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"Institute for Glycomics and School of Information and Communication Technology, Griffith University, Southport, QLD, 4215, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210112812","display_name":"National Supercomputing Center in Shenzhen","ror":"https://ror.org/02291hh73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210112812"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China. yangyd25@mail.sysu.edu.cn","National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China"],"raw_orcid":"https://orcid.org/0000-0002-6782-2813","affiliations":[{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China. yangyd25@mail.sysu.edu.cn","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"National Supercomputer Center in Guangzhou, School of Data and Computer Science, Sun Yat-sen University, 132 East Circle at University City, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I4210112812","https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5029051152","https://openalex.org/A5032724151"],"corresponding_institution_ids":["https://openalex.org/I11701301","https://openalex.org/I157773358","https://openalex.org/I4210097354"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":7.0752,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.9743001,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"52","last_page":"52"},"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":0.9977999925613403,"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":0.9965000152587891,"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":0.7309606671333313},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5283782482147217},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.5128529071807861},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.47031891345977783},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.44641435146331787},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41124987602233887},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39858338236808777},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3619116544723511},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1828429400920868},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.16814866662025452},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.14326411485671997},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.09780934453010559}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7309606671333313},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5283782482147217},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5128529071807861},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.47031891345977783},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.44641435146331787},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41124987602233887},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39858338236808777},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3619116544723511},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1828429400920868},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.16814866662025452},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.14326411485671997},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.09780934453010559},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-019-0373-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0373-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0373-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:31392430","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31392430","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 cheminformatics","raw_type":null},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/390181","is_oa":true,"landing_page_url":"http://hdl.handle.net/10072/390181","pdf_url":"http://hdl.handle.net/10072/390181","source":{"id":"https://openalex.org/S4306402548","display_name":"Griffith Research Online (Griffith University, Queensland, Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11701301","host_organization_name":"Griffith University","host_organization_lineage":["https://openalex.org/I11701301"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"},{"id":"pmh:oai:doaj.org/article:687173ee8201457da96792197b2c54b8","is_oa":true,"landing_page_url":"https://doaj.org/article/687173ee8201457da96792197b2c54b8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-11 (2019)","raw_type":"article"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:e281eea","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5640280","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6686496","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-019-0373-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0373-4","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0373-4","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8700000047683716,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1065191731","display_name":null,"funder_award_id":"1121629","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"},{"id":"https://openalex.org/G1114770080","display_name":null,"funder_award_id":"DP180102060","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G1619931070","display_name":null,"funder_award_id":"U1611261","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4285831925","display_name":null,"funder_award_id":"81801132","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4917514995","display_name":null,"funder_award_id":"2018YFC0910500","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5108781970","display_name":null,"funder_award_id":"61772566","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6346021793","display_name":null,"funder_award_id":"2019B020228001","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/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2964549872.pdf","grobid_xml":"https://content.openalex.org/works/W2964549872.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1539947917","https://openalex.org/W1573009101","https://openalex.org/W1605578858","https://openalex.org/W1965207004","https://openalex.org/W1968319881","https://openalex.org/W1969017960","https://openalex.org/W1980120676","https://openalex.org/W1981500172","https://openalex.org/W1985588649","https://openalex.org/W1998568556","https://openalex.org/W1999359666","https://openalex.org/W2001722230","https://openalex.org/W2004595546","https://openalex.org/W2009423060","https://openalex.org/W2013085020","https://openalex.org/W2014704001","https://openalex.org/W2025116694","https://openalex.org/W2040990879","https://openalex.org/W2044444984","https://openalex.org/W2049185580","https://openalex.org/W2053759741","https://openalex.org/W2073021822","https://openalex.org/W2075020622","https://openalex.org/W2076556722","https://openalex.org/W2079331631","https://openalex.org/W2092285329","https://openalex.org/W2098312592","https://openalex.org/W2105527266","https://openalex.org/W2105668062","https://openalex.org/W2117109292","https://openalex.org/W2118587156","https://openalex.org/W2122401542","https://openalex.org/W2125677968","https://openalex.org/W2126714395","https://openalex.org/W2128332459","https://openalex.org/W2134967712","https://openalex.org/W2138015848","https://openalex.org/W2142868265","https://openalex.org/W2148512505","https://openalex.org/W2156558709","https://openalex.org/W2158360182","https://openalex.org/W2158714788","https://openalex.org/W2166765429","https://openalex.org/W2169562071","https://openalex.org/W2170116275","https://openalex.org/W2262896633","https://openalex.org/W2314626150","https://openalex.org/W2334483166","https://openalex.org/W2346236193","https://openalex.org/W2492804765","https://openalex.org/W2512819857","https://openalex.org/W2521525223","https://openalex.org/W2550887636","https://openalex.org/W2567812636","https://openalex.org/W2588514765","https://openalex.org/W2608559058","https://openalex.org/W2613541742","https://openalex.org/W2625186389","https://openalex.org/W2808950571","https://openalex.org/W2923747700","https://openalex.org/W2952663663"],"related_works":["https://openalex.org/W4241081643","https://openalex.org/W1974414168","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2093426296","https://openalex.org/W2336040088","https://openalex.org/W2038399774","https://openalex.org/W2750247885"],"abstract_inverted_index":{"Performance":[0],"of":[1,10,16,27,56],"structure-based":[2],"molecular":[3],"docking":[4,198],"largely":[5],"depends":[6],"on":[7,43,124,159],"the":[8,54,85,125,167,172,182,194],"accuracy":[9],"scoring":[11,17,207],"functions.":[12,208],"One":[13],"important":[14],"type":[15],"functions":[18,139],"are":[19,163],"knowledge-based":[20,39],"potentials":[21],"derived":[22],"from":[23,59],"known":[24],"three-dimensional":[25],"structures":[26,103],"proteins":[28],"and/or":[29],"protein-ligand":[30,40],"complex":[31,102],"structures.":[32],"This":[33],"study":[34],"seeks":[35],"to":[36,64,166],"improve":[37],"a":[38,44,71,90,111,176],"potential":[41,179],"based":[42,123],"distance-scale":[45],"finite":[46],"ideal-gas":[47],"reference":[48],"(DFIRE)":[49],"state":[50],"(DLIGAND)":[51],"by":[52,197],"expanding":[53],"representation":[55],"protein":[57,78],"atoms":[58],"13":[60],"mol2":[61],"atom":[62,67],"types":[63],"167":[65],"residue-specific":[66],"types,":[68],"and":[69,129,135,152,180],"employing":[70],"recently":[72],"updated":[73,86],"dataset":[74],"containing":[75],"12,450":[76],"monomer":[77],"chains":[79],"for":[80,99,156,192],"training.":[81],"We":[82,145],"found":[83,147],"that":[84,148,162],"version":[87],"DLIGAND2":[88,109,149,188],"has":[89,110],"consistent":[91],"improvement":[92],"over":[93,114,132],"DLIGAND":[94,115],"in":[95,116,119,140,184,205],"predicting":[96],"binding":[97],"affinities":[98],"either":[100],"native":[101],"or":[104,200],"docking-generated":[105],"poses.":[106],"More":[107],"importantly,":[108],"52%":[112],"increase":[113],"enrichment":[117],"factors":[118],"top":[120],"1%":[121],"predictions":[122],"DUD-E":[126,168],"decoy":[127],"set,":[128],"consistently":[130],"improves":[131],"Autodock":[133],"Vina":[134],"other":[136,206],"statistical":[137,178],"energy":[138],"all":[141,185],"three":[142],"benchmark":[143],"tests.":[144],"further":[146],"outperforms":[150],"empirical":[151],"machine-learning":[153],"methods":[154],"compared":[155],"virtual":[157],"screening":[158],"new":[160],"targets":[161],"not":[164],"homologous":[165],"training":[169],"set.":[170],"Given":[171],"best":[173,183],"performance":[174,186],"as":[175,202],"parameter-free":[177],"among":[181],"measures,":[187],"should":[189],"be":[190],"useful":[191],"re-assessing":[193],"poses":[195],"generated":[196],"software,":[199],"acting":[201],"one":[203],"term":[204],"The":[209],"program":[210],"is":[211],"available":[212],"at":[213],"https://github.com/sysu-yanglab/DLIGAND2":[214],".":[215]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
