{"id":"https://openalex.org/W3030054993","doi":"https://doi.org/10.1186/s13321-020-00440-9","title":"EDock: blind protein\u2013ligand docking by replica-exchange monte carlo simulation","display_name":"EDock: blind protein\u2013ligand docking by replica-exchange monte carlo simulation","publication_year":2020,"publication_date":"2020-05-27","ids":{"openalex":"https://openalex.org/W3030054993","doi":"https://doi.org/10.1186/s13321-020-00440-9","mag":"3030054993","pmid":"https://pubmed.ncbi.nlm.nih.gov/33430966"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-020-00440-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00440-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00440-9","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/s13321-020-00440-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100360025","display_name":"Wenyi Zhang","orcid":"https://orcid.org/0000-0002-5514-9676"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Wenyi Zhang","raw_affiliation_strings":["College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China","Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA"],"raw_orcid":"https://orcid.org/0000-0002-5514-9676","affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China","institution_ids":["https://openalex.org/I184983240"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035236057","display_name":"Eric W. Bell","orcid":"https://orcid.org/0000-0002-3419-4398"},"institutions":[{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric W. Bell","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023555343","display_name":"Minghao Yin","orcid":"https://orcid.org/0000-0002-6226-2394"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minghao Yin","raw_affiliation_strings":["College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China. ymh@nenu.edu.cn","College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China. ymh@nenu.edu.cn","institution_ids":["https://openalex.org/I184983240"]},{"raw_affiliation_string":"College of Information Science and Technology, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I199037182","display_name":"Washtenaw Community College","ror":"https://ror.org/03k77wm53","country_code":"US","type":"education","lineage":["https://openalex.org/I199037182"]},{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109-2218, USA. zhng@umich.edu","Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA. zhng@umich.edu","Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA"],"raw_orcid":"https://orcid.org/0000-0002-2739-1916","affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109-2218, USA. zhng@umich.edu","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA. zhng@umich.edu","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA","institution_ids":["https://openalex.org/I199037182","https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5023555343","https://openalex.org/A5100354659"],"corresponding_institution_ids":["https://openalex.org/I184983240","https://openalex.org/I199037182","https://openalex.org/I27837315","https://openalex.org/I4210114445"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":6.354,"has_fulltext":true,"cited_by_count":100,"citation_normalized_percentile":{"value":0.97119565,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"12","issue":"1","first_page":"37","last_page":"37"},"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":0.9961000084877014,"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/T11162","display_name":"Enzyme Structure and Function","score":0.982200026512146,"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/docking","display_name":"Docking (animal)","score":0.7710781097412109},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.7137565016746521},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.6866776943206787},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5976152420043945},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.5719158053398132},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.546738862991333},{"id":"https://openalex.org/keywords/replica","display_name":"Replica","score":0.5023758411407471},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.4728263318538666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36304971575737},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34195539355278015},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2997073233127594},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.28698447346687317},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.19094020128250122},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.1687839925289154},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14223039150238037},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11162540316581726},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.10698792338371277}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7710781097412109},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.7137565016746521},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.6866776943206787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5976152420043945},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.5719158053398132},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.546738862991333},{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.5023758411407471},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.4728263318538666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36304971575737},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34195539355278015},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2997073233127594},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.28698447346687317},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.19094020128250122},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.1687839925289154},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14223039150238037},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11162540316581726},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.10698792338371277},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","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/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-020-00440-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00440-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00440-9","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:33430966","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33430966","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:deepblue.lib.umich.edu:2027.42/173878","is_oa":false,"landing_page_url":"https://hdl.handle.net/2027.42/173878","pdf_url":null,"source":{"id":"https://openalex.org/S4306400393","display_name":"Deep Blue (University of Michigan)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I27837315","host_organization_name":"University of Michigan","host_organization_lineage":["https://openalex.org/I27837315"],"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":"Journal Article"},{"id":"pmh:oai:doaj.org/article:2fb804b5bd374f0e83d123ac0eaebabc","is_oa":true,"landing_page_url":"https://doaj.org/article/2fb804b5bd374f0e83d123ac0eaebabc","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 12, Iss 1, Pp 1-17 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7251717","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7251717","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-020-00440-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-020-00440-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00440-9","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":[{"score":0.5,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G1977669034","display_name":null,"funder_award_id":"IIS1901191","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":"XSEDE 2.0:  Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement","funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4361546247","display_name":null,"funder_award_id":"201606620076","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G4584606584","display_name":null,"funder_award_id":"GM136422","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7063014021","display_name":null,"funder_award_id":"AI134678","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G748008874","display_name":null,"funder_award_id":"DBI1564756","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G758395984","display_name":null,"funder_award_id":"R35 GM136422","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7747661902","display_name":null,"funder_award_id":"DBI1564756","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8600038702","display_name":null,"funder_award_id":"IIS1901191","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3030054993.pdf","grobid_xml":"https://content.openalex.org/works/W3030054993.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1985588649","https://openalex.org/W1986240377","https://openalex.org/W1987134040","https://openalex.org/W2013145865","https://openalex.org/W2015688756","https://openalex.org/W2018530279","https://openalex.org/W2018661561","https://openalex.org/W2042572511","https://openalex.org/W2050456292","https://openalex.org/W2052963427","https://openalex.org/W2056760934","https://openalex.org/W2068465600","https://openalex.org/W2078374001","https://openalex.org/W2102245393","https://openalex.org/W2105792689","https://openalex.org/W2108107014","https://openalex.org/W2111767148","https://openalex.org/W2128332459","https://openalex.org/W2131288855","https://openalex.org/W2132395520","https://openalex.org/W2134967712","https://openalex.org/W2139281871","https://openalex.org/W2140538197","https://openalex.org/W2144258433","https://openalex.org/W2146233784","https://openalex.org/W2161151688","https://openalex.org/W2789748145","https://openalex.org/W2954297401"],"related_works":["https://openalex.org/W2089188080","https://openalex.org/W2109587698","https://openalex.org/W3200294295","https://openalex.org/W2138402460","https://openalex.org/W2136513242","https://openalex.org/W4210495387","https://openalex.org/W3020829968","https://openalex.org/W2057055220","https://openalex.org/W2336040088","https://openalex.org/W4245963358"],"abstract_inverted_index":{"Protein-ligand":[0],"docking":[1,15,55,174,196,261],"is":[2,71],"an":[3],"important":[4,51],"approach":[5],"for":[6,42,86,121,235],"virtual":[7],"screening":[8],"and":[9,29,61,101,180,203,208,229,251,254],"protein":[10,68,264],"function":[11],"annotation.":[12],"Although":[13],"many":[14,49],"methods":[16,56,175],"have":[17],"been":[18],"developed,":[19],"most":[20],"require":[21],"a":[22,30,79,91,129,163,199],"high-resolution":[23],"crystal":[24],"structure":[25,69],"of":[26,45,128,166,220,238,248,259],"the":[27,43,126,155,217,236,257],"receptor":[28,65,157],"user-specified":[31],"binding":[32,59,94,152,226],"site":[33,227],"to":[34,244],"start.":[35],"This":[36],"information":[37],"is,":[38],"however,":[39],"not":[40],"available":[41],"majority":[44],"unknown":[46],"proteins,":[47],"including":[48,176],"pharmaceutically":[50],"targets.":[52],"Developing":[53],"blind":[54,87],"without":[57],"predefined":[58],"sites":[60,95],"working":[62],"with":[63,105,134,172,187,198,262],"low-resolution":[64,260],"models":[66,189],"from":[67,190],"prediction":[70],"thus":[72],"essential.":[73],"In":[74],"this":[75],"manuscript,":[76],"we":[77],"propose":[78],"novel":[80],"Monte":[81,115],"Carlo":[82,116],"based":[83],"method,":[84],"EDock,":[85],"protein-ligand":[88,148],"docking.":[89],"For":[90],"given":[92],"protein,":[93],"are":[96,119],"first":[97],"predicted":[98,188,263],"by":[99,110],"sequence-profile":[100],"substructure-based":[102],"comparison":[103],"searches":[104],"initial":[106],"ligand":[107,122,164,225],"poses":[108],"generated":[109],"graph":[111],"matching.":[112],"Next,":[113],"replica-exchange":[114],"(REMC)":[117],"simulations":[118],"performed":[120],"conformation":[123],"refinement":[124],"under":[125],"guidance":[127],"physical":[130],"force":[131],"field":[132],"coupled":[133],"binding-site":[135],"distance":[136],"constraints.":[137],"The":[138],"method":[139],"was":[140],"tested":[141],"on":[142,154,161],"two":[143],"large-scale":[144],"datasets":[145],"containing":[146],"535":[147],"pairs.":[149],"Without":[150],"specifying":[151],"pockets":[153],"experimental":[156],"structures,":[158],"EDock":[159,192,221],"achieves":[160],"average":[162],"RMSD":[165],"2.03":[167],"\u00c5,":[168],"which":[169,233],"compares":[170],"favorably":[171],"state-of-the-art":[173],"DOCK6":[177,207],"(2.68":[178],"\u00c5)":[179],"AutoDock":[181,209],"Vina":[182],"(3.92":[183],"\u00c5).":[184],"When":[185],"starting":[186],"I-TASSER,":[191],"still":[193],"generates":[194],"reasonable":[195],"models,":[197],"success":[200],"rate":[201],"159%":[202],"67%":[204],"higher":[205],"than":[206],"Vina,":[210],"respectively.":[211],"Detailed":[212],"data":[213],"analyses":[214],"show":[215],"that":[216],"major":[218],"advantage":[219],"lies":[222],"in":[223],"reliable":[224],"predictions":[228],"extensive":[230],"REMC":[231],"sampling,":[232],"allows":[234],"implementation":[237],"multiple":[239],"van":[240],"der":[241],"Waals":[242],"weightings":[243],"accommodate":[245],"different":[246],"levels":[247],"steric":[249],"clashes":[250],"cavity":[252],"distortions":[253],"therefore":[255],"enhances":[256],"robustness":[258],"structures.":[265]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
