{"id":"https://openalex.org/W2999342780","doi":"https://doi.org/10.1021/acs.jcim.9b00905","title":"Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein\u2013Peptide Data Set","display_name":"Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein\u2013Peptide Data Set","publication_year":2020,"publication_date":"2020-01-10","ids":{"openalex":"https://openalex.org/W2999342780","doi":"https://doi.org/10.1021/acs.jcim.9b00905","mag":"2999342780","pmid":"https://pubmed.ncbi.nlm.nih.gov/31922754"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00905","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00905","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/A5013063323","display_name":"Karina B. Santos","orcid":"https://orcid.org/0000-0001-9202-4584"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Karina B. Santos","raw_affiliation_strings":["National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008226082","display_name":"Isabella Alvim Guedes","orcid":"https://orcid.org/0000-0002-9761-4804"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Isabella A. Guedes","raw_affiliation_strings":["National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-9761-4804","affiliations":[{"raw_affiliation_string":"National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025150028","display_name":"Ana L. M. Karl","orcid":"https://orcid.org/0000-0002-9071-2831"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ana L. M. Karl","raw_affiliation_strings":["National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084969079","display_name":"Laurent E. Dardenne","orcid":"https://orcid.org/0000-0001-8518-8062"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Laurent E. Dardenne","raw_affiliation_strings":["National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-8518-8062","affiliations":[{"raw_affiliation_string":"National Laboratory for Scientific Computing - LNCC, Petr\u00f3polis, Rio de Janeiro 25651-075, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5084969079"],"corresponding_institution_ids":["https://openalex.org/I4210142352"],"apc_list":null,"apc_paid":null,"fwci":23.2668,"has_fulltext":false,"cited_by_count":269,"citation_normalized_percentile":{"value":0.99624373,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"60","issue":"2","first_page":"667","last_page":"683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9979000091552734,"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":0.9979000091552734,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9952999949455261,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9879000186920166,"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":0.9138767719268799},{"id":"https://openalex.org/keywords/autodock","display_name":"AutoDock","score":0.839966893196106},{"id":"https://openalex.org/keywords/protein\u2013ligand-docking","display_name":"Protein\u2013ligand docking","score":0.742034912109375},{"id":"https://openalex.org/keywords/dock","display_name":"DOCK","score":0.7351314425468445},{"id":"https://openalex.org/keywords/searching-the-conformational-space-for-docking","display_name":"Searching the conformational space for docking","score":0.6783117055892944},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46649834513664246},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.4539986252784729},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.4459265470504761},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41126328706741333},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.36879435181617737},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3335178792476654},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.2979327440261841},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.25056737661361694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15249115228652954},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.152387797832489}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.9138767719268799},{"id":"https://openalex.org/C2780152424","wikidata":"https://www.wikidata.org/wiki/Q4826062","display_name":"AutoDock","level":4,"score":0.839966893196106},{"id":"https://openalex.org/C77319485","wikidata":"https://www.wikidata.org/wiki/Q7251520","display_name":"Protein\u2013ligand docking","level":4,"score":0.742034912109375},{"id":"https://openalex.org/C93073132","wikidata":"https://www.wikidata.org/wiki/Q24726581","display_name":"DOCK","level":2,"score":0.7351314425468445},{"id":"https://openalex.org/C44695244","wikidata":"https://www.wikidata.org/wiki/Q7441727","display_name":"Searching the conformational space for docking","level":3,"score":0.6783117055892944},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46649834513664246},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.4539986252784729},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.4459265470504761},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41126328706741333},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.36879435181617737},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3335178792476654},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2979327440261841},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.25056737661361694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15249115228652954},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.152387797832489},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"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/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","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/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00905","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00905","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:31922754","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31922754","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":[],"awards":[{"id":"https://openalex.org/G1453094054","display_name":null,"funder_award_id":"308202/2016-3","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G2880474677","display_name":null,"funder_award_id":"300463/2019-7","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G6405090189","display_name":null,"funder_award_id":"E-26/010.001415/2019","funder_id":"https://openalex.org/F4320322749","funder_display_name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro"},{"id":"https://openalex.org/G7639798870","display_name":null,"funder_award_id":"312604/2016-5","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G819525903","display_name":null,"funder_award_id":"E-26/010.001229/2015","funder_id":"https://openalex.org/F4320322749","funder_display_name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro"}],"funders":[{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322749","display_name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","ror":"https://ror.org/03kk0s825"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":86,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1860382351","https://openalex.org/W1881444267","https://openalex.org/W1941251942","https://openalex.org/W1964958542","https://openalex.org/W1972043325","https://openalex.org/W1980653863","https://openalex.org/W1981021420","https://openalex.org/W1985588649","https://openalex.org/W1990166538","https://openalex.org/W1990724722","https://openalex.org/W2007714946","https://openalex.org/W2008518939","https://openalex.org/W2008708467","https://openalex.org/W2009400274","https://openalex.org/W2018989832","https://openalex.org/W2019732485","https://openalex.org/W2020446183","https://openalex.org/W2023272942","https://openalex.org/W2023724309","https://openalex.org/W2027423337","https://openalex.org/W2031168104","https://openalex.org/W2044444984","https://openalex.org/W2050456292","https://openalex.org/W2052568158","https://openalex.org/W2053174787","https://openalex.org/W2054954101","https://openalex.org/W2056189051","https://openalex.org/W2067712920","https://openalex.org/W2072180710","https://openalex.org/W2073306537","https://openalex.org/W2081992461","https://openalex.org/W2102377211","https://openalex.org/W2105668062","https://openalex.org/W2115318272","https://openalex.org/W2119636371","https://openalex.org/W2122874479","https://openalex.org/W2123742735","https://openalex.org/W2125497220","https://openalex.org/W2126103104","https://openalex.org/W2128629409","https://openalex.org/W2130479394","https://openalex.org/W2132928818","https://openalex.org/W2134967712","https://openalex.org/W2140210268","https://openalex.org/W2142529984","https://openalex.org/W2143094533","https://openalex.org/W2144935199","https://openalex.org/W2147421370","https://openalex.org/W2153594105","https://openalex.org/W2169678694","https://openalex.org/W2233834908","https://openalex.org/W2293547369","https://openalex.org/W2330799739","https://openalex.org/W2342678031","https://openalex.org/W2503220818","https://openalex.org/W2527938699","https://openalex.org/W2554109484","https://openalex.org/W2588284375","https://openalex.org/W2594502287","https://openalex.org/W2594877435","https://openalex.org/W2600436070","https://openalex.org/W2609643846","https://openalex.org/W2626090269","https://openalex.org/W2724823461","https://openalex.org/W2727656886","https://openalex.org/W2739980134","https://openalex.org/W2767812299","https://openalex.org/W2768968558","https://openalex.org/W2794491987","https://openalex.org/W2794774007","https://openalex.org/W2799876761","https://openalex.org/W2800677598","https://openalex.org/W2802186587","https://openalex.org/W2893435209","https://openalex.org/W2902812092","https://openalex.org/W2911741628","https://openalex.org/W2921974962","https://openalex.org/W2948831670","https://openalex.org/W2948988173","https://openalex.org/W2952059807","https://openalex.org/W2955254529","https://openalex.org/W2969826342","https://openalex.org/W2972038757","https://openalex.org/W2972485984","https://openalex.org/W4210290639"],"related_works":["https://openalex.org/W3199423294","https://openalex.org/W4248527317","https://openalex.org/W2969945877","https://openalex.org/W2058674645","https://openalex.org/W2766845742","https://openalex.org/W2477070048","https://openalex.org/W2068609125","https://openalex.org/W2100436540","https://openalex.org/W2117109292","https://openalex.org/W2149658535"],"abstract_inverted_index":{"Protein-peptide":[0],"interactions":[1],"play":[2],"a":[3,34,73,198,242],"crucial":[4],"role":[5],"in":[6,17,30,203],"many":[7],"cellular":[8],"and":[9,28,90,129,171,179,228],"biological":[10],"functions,":[11],"which":[12],"justify":[13],"the":[14,18,52,62,65,69,118,135,149,160,185,190,208,216],"increasing":[15],"interest":[16],"development":[19],"of":[20,45,48,55,64,77,148,201,212],"peptide-based":[21],"drugs.":[22],"However,":[23],"predicting":[24],"experimental":[25],"binding":[26],"modes":[27],"affinities":[29],"protein-peptide":[31,80],"docking":[32,39,111,137,162,175,186,225],"remains":[33],"great":[35,209],"challenge":[36],"for":[37,100,224],"most":[38],"programs":[40,112],"due":[41],"to":[42,87,93,169,189,207,233],"some":[43,109],"particularities":[44],"this":[46,58],"class":[47],"ligands,":[49,230],"such":[50],"as":[51,131,133,222,241],"high":[53],"degree":[54],"flexibility.":[56],"In":[57],"paper,":[59],"we":[60],"present":[61],"performance":[63,99,211],"DockThor":[66,98,144,196,217,237],"program":[67,218],"on":[68,103,117],"LEADS-PEP":[70,119],"data":[71,120],"set,":[72,121],"benchmarking":[74],"set":[75],"composed":[76],"53":[78],"diverse":[79],"complexes":[81],"with":[82,91,108,134,151,231],"peptides":[83],"ranging":[84],"from":[85],"3":[86],"12":[88],"residues":[89],"up":[92,232],"51":[94],"rotatable":[95,235],"bonds.":[96,236],"The":[97],"pose":[101,163,204],"prediction":[102],"redocking":[104],"studies":[105],"was":[106,164],"compared":[107],"state-of-the-art":[110],"that":[113,143],"were":[114],"also":[115],"evaluated":[116],"AutoDock,":[122],"AutoDock":[123],"Vina,":[124],"Surflex,":[125],"GOLD,":[126],"Glide,":[127],"rDock,":[128],"DINC,":[130],"well":[132],"task-specific":[136],"protocol":[138],"HPepDock.":[139],"Our":[140],"results":[141,168],"indicate":[142],"could":[145],"dock":[146],"40%":[147],"cases":[150],"an":[152],"overall":[153,210],"backbone":[154],"RMSD":[155],"below":[156],"2.5":[157],"\u00c5":[158],"when":[159],"top-scored":[161],"considered,":[165],"exhibiting":[166],"similar":[167],"Glide":[170],"outperforming":[172],"other":[173],"protein-ligand":[174],"programs,":[176],"whereas":[177],"rDock":[178],"HPepDock":[180],"achieved":[181,197],"superior":[182],"results.":[183],"Assessing":[184],"poses":[187],"closest":[188],"crystal":[191],"structure":[192],"(i.e.,":[193],"best-RMSD":[194],"pose),":[195],"success":[199],"rate":[200],"60%":[202],"prediction.":[205],"Due":[206],"handling":[213],"peptidic":[214],"compounds,":[215],"can":[219],"be":[220],"considered":[221],"suitable":[223],"highly":[226],"flexible":[227],"challenging":[229],"40":[234],"is":[238],"freely":[239],"available":[240],"virtual":[243],"screening":[244],"Web":[245],"server":[246],"at":[247],"https://www.dockthor.lncc.br/":[248],".":[249]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":41},{"year":2024,"cited_by_count":57},{"year":2023,"cited_by_count":55},{"year":2022,"cited_by_count":43},{"year":2021,"cited_by_count":45},{"year":2020,"cited_by_count":18}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}