{"id":"https://openalex.org/W4388132002","doi":"https://doi.org/10.1186/s13321-023-00772-2","title":"EasyDock: customizable and scalable docking tool","display_name":"EasyDock: customizable and scalable docking tool","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388132002","doi":"https://doi.org/10.1186/s13321-023-00772-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/37915072"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00772-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00772-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00772-2","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/counter/pdf/10.1186/s13321-023-00772-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Guzel Minibaeva","orcid":null},"institutions":[{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]},{"id":"https://openalex.org/I4210146721","display_name":"Institute of Molecular and Translational Medicine","ror":"https://ror.org/041e7q719","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I4210146721"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Guzel Minibaeva","raw_affiliation_strings":["Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I4210146721","https://openalex.org/I70703428"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067783752","display_name":"Aleksandra Ivanov\u00e1","orcid":"https://orcid.org/0000-0002-8064-7845"},"institutions":[{"id":"https://openalex.org/I4210146721","display_name":"Institute of Molecular and Translational Medicine","ror":"https://ror.org/041e7q719","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I4210146721"]},{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Aleksandra Ivanova","raw_affiliation_strings":["Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I4210146721","https://openalex.org/I70703428"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080175337","display_name":"Pavel Polishchuk","orcid":"https://orcid.org/0000-0001-5088-8149"},"institutions":[{"id":"https://openalex.org/I70703428","display_name":"Palack\u00fd University Olomouc","ror":"https://ror.org/04qxnmv42","country_code":"CZ","type":"education","lineage":["https://openalex.org/I70703428"]},{"id":"https://openalex.org/I4210146721","display_name":"Institute of Molecular and Translational Medicine","ror":"https://ror.org/041e7q719","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I4210146721"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Pavel Polishchuk","raw_affiliation_strings":["Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic. pavlo.polishchuk@upol.cz","Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic"],"affiliations":[{"raw_affiliation_string":"Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic. pavlo.polishchuk@upol.cz","institution_ids":[]},{"raw_affiliation_string":"Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University and University Hospital in Olomouc, Hnevotinska 5, 77900, Olomouc, Czech Republic","institution_ids":["https://openalex.org/I4210146721","https://openalex.org/I70703428"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210146721","https://openalex.org/I70703428"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":4.2811,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.95359952,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"15","issue":"1","first_page":"102","last_page":"102"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9973000288009644,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9908000230789185,"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/docking","display_name":"Docking (animal)","score":0.8072202205657959},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7567975521087646},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6509703397750854},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.513976514339447},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.4332825541496277},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3929770588874817},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.29991352558135986},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.2689793109893799},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.18794643878936768},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17528799176216125},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1477660834789276}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8072202205657959},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7567975521087646},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6509703397750854},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.513976514339447},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.4332825541496277},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3929770588874817},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.29991352558135986},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2689793109893799},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.18794643878936768},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17528799176216125},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1477660834789276},{"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/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"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/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00772-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00772-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00772-2","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:37915072","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37915072","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:pubmedcentral.nih.gov:10619229","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10619229","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10619229/pdf/13321_2023_Article_772.pdf","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"},{"id":"pmh:oai:doaj.org/article:3a7d632969544228a1e857f6137518e0","is_oa":true,"landing_page_url":"https://doaj.org/article/3a7d632969544228a1e857f6137518e0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-11 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00772-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00772-2","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00772-2","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":0.6200000047683716,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G5333091627","display_name":null,"funder_award_id":"LUAUS23262","funder_id":"https://openalex.org/F4320321005","funder_display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy"},{"id":"https://openalex.org/G6321423191","display_name":null,"funder_award_id":"CZ.02.1.01/0.0/0.0/16_019/0000868","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"}],"funders":[{"id":"https://openalex.org/F4320321005","display_name":"Ministerstvo \u0160kolstv\u00ed, Ml\u00e1de\u017ee a T\u011blov\u00fdchovy","ror":"https://ror.org/037n8p820"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388132002.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1607931568","https://openalex.org/W1800166884","https://openalex.org/W1973739281","https://openalex.org/W1981419696","https://openalex.org/W2011658408","https://openalex.org/W2023818227","https://openalex.org/W2026501977","https://openalex.org/W2028629022","https://openalex.org/W2042192709","https://openalex.org/W2045731972","https://openalex.org/W2046588282","https://openalex.org/W2119923393","https://openalex.org/W2132629607","https://openalex.org/W2388080941","https://openalex.org/W2527672088","https://openalex.org/W2912171584","https://openalex.org/W2920995682","https://openalex.org/W3010016408","https://openalex.org/W3094428287","https://openalex.org/W3124667367","https://openalex.org/W3126424190","https://openalex.org/W3168430821","https://openalex.org/W3168436232","https://openalex.org/W3201539868","https://openalex.org/W3208515103","https://openalex.org/W3212543990","https://openalex.org/W4200233821","https://openalex.org/W4211196614","https://openalex.org/W4211218744","https://openalex.org/W4214686850","https://openalex.org/W4214934254","https://openalex.org/W4224140425","https://openalex.org/W4313552198"],"related_works":["https://openalex.org/W2336040088","https://openalex.org/W2136513242","https://openalex.org/W2766845742","https://openalex.org/W2058674645","https://openalex.org/W4385073511","https://openalex.org/W1594539819","https://openalex.org/W3113038228","https://openalex.org/W3199423294","https://openalex.org/W2007257620","https://openalex.org/W2614191518"],"abstract_inverted_index":{"Docking":[0],"of":[1,15,18,44,50,68,82,128,154,168,189,208],"large":[2,16,48],"compound":[3],"collections":[4],"becomes":[5],"an":[6],"important":[7],"procedure":[8],"to":[9,78,111,160,186],"discover":[10],"new":[11,69],"chemical":[12],"entities.":[13],"Screening":[14],"sets":[17],"compounds":[19],"may":[20],"also":[21,63],"occur":[22],"in":[23],"de":[24],"novo":[25],"design":[26],"projects":[27],"guided":[28],"by":[29,197],"molecular":[30],"docking.":[31],"To":[32],"facilitate":[33],"these":[34,112],"processes,":[35],"there":[36],"is":[37],"a":[38,47,57,74,88,99,117,126,137,147,183,206],"need":[39],"for":[40,65,106],"automated":[41],"tools":[42,61,92],"capable":[43],"efficiently":[45],"docking":[46,70,86,155,163,172,188],"number":[49],"molecules":[51],"using":[52,131],"multiple":[53],"computational":[54,129],"nodes":[55,130],"within":[56],"reasonable":[58],"timeframe.":[59],"These":[60],"should":[62],"allow":[64],"easy":[66],"integration":[67],"programs":[71],"and":[72,145,157,178,199,201],"provide":[73],"user-friendly":[75],"program":[76,101],"interface":[77,102],"support":[79,105],"the":[80,132,152],"development":[81],"further":[83],"approaches":[84],"utilizing":[85],"as":[87,97],"foundation.":[89],"Currently":[90],"available":[91],"have":[93,115,143],"certain":[94],"limitations,":[95,113],"such":[96],"lacking":[98,104],"convenient":[100],"or":[103],"distributed":[107],"computations.":[108],"In":[109],"response":[110],"we":[114,142,181],"developed":[116],"module":[118],"called":[119],"EasyDock.":[120],"It":[121],"can":[122],"be":[123],"deployed":[124],"over":[125],"network":[127],"Dask":[133],"library,":[134],"without":[135],"requiring":[136],"specific":[138],"cluster":[139],"scheduler.":[140],"Furthermore,":[141],"proposed":[144],"implemented":[146,182],"simple":[148],"model":[149],"that":[150],"predicts":[151],"runtime":[153],"experiments":[156],"applied":[158],"it":[159],"minimize":[161],"overall":[162],"time.":[164],"The":[165],"current":[166],"version":[167],"EasyDock":[169],"supports":[170],"popular":[171],"programs,":[173],"namely":[174],"Autodock":[175],"Vina,":[176],"gnina,":[177],"smina.":[179],"Additionally,":[180],"supplementary":[184],"feature":[185],"enable":[187],"boron-containing":[190],"compounds,":[191],"which":[192],"are":[193],"not":[194],"inherently":[195],"supported":[196],"Vina":[198],"smina,":[200],"demonstrated":[202],"its":[203],"applicability":[204],"on":[205],"set":[207],"55":[209],"PDB":[210],"protein-ligand":[211],"complexes.":[212]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":10}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
