{"id":"https://openalex.org/W2086126241","doi":"https://doi.org/10.1021/ci400094h","title":"Application of the Docking Program SOL for CSAR Benchmark","display_name":"Application of the Docking Program SOL for CSAR Benchmark","publication_year":2013,"publication_date":"2013-07-05","ids":{"openalex":"https://openalex.org/W2086126241","doi":"https://doi.org/10.1021/ci400094h","mag":"2086126241","pmid":"https://pubmed.ncbi.nlm.nih.gov/23829357"},"language":"en","primary_location":{"id":"doi:10.1021/ci400094h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400094h","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/A5101695175","display_name":"\u0410.\u0412. \u0421\u0443\u043b\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0002-8767-642X"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Alexey V. Sulimov","raw_affiliation_strings":["Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg 4, Moscow 119992, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg 4, Moscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081004260","display_name":"Danil Kutov","orcid":"https://orcid.org/0000-0002-4777-6522"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Danil C. Kutov","raw_affiliation_strings":["Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg 4, Moscow 119992, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, Bldg 4, Moscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065039087","display_name":"I. V. Oferkin","orcid":null},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Igor V. Oferkin","raw_affiliation_strings":["Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021128272","display_name":"E. V. Katkova","orcid":"https://orcid.org/0000-0001-9961-4069"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ekaterina V. Katkova","raw_affiliation_strings":["Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080885688","display_name":"\u0412. \u0411. \u0421\u0443\u043b\u0438\u043c\u043e\u0432","orcid":"https://orcid.org/0000-0002-7102-6107"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"Vladimir B. Sulimov","raw_affiliation_strings":["Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dimonta, Ltd., Nagornaya Street 15, bldg 8, Moscow\r117186, Russia","institution_ids":[]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,\rMoscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]},{"raw_affiliation_string":"Research Computer Center, Moscow State University, Leninskie Gory 1, bldg 4,#R#Moscow 119992, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5080885688"],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":4.0097,"has_fulltext":false,"cited_by_count":50,"citation_normalized_percentile":{"value":0.93959184,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"53","issue":"8","first_page":"1946","last_page":"1956"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9803000092506409,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9282000064849854,"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":0.8093142509460449},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6133227348327637},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6054152250289917},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5250689387321472},{"id":"https://openalex.org/keywords/target-protein","display_name":"Target protein","score":0.4156065285205841},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3371945917606354},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.26792263984680176},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1018424928188324},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09967932105064392},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08313414454460144},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07263776659965515}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.8093142509460449},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6133227348327637},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6054152250289917},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5250689387321472},{"id":"https://openalex.org/C2780430158","wikidata":"https://www.wikidata.org/wiki/Q7685902","display_name":"Target protein","level":3,"score":0.4156065285205841},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3371945917606354},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.26792263984680176},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1018424928188324},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09967932105064392},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08313414454460144},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07263776659965515},{"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019540","descriptor_name":"Area Under Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci400094h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400094h","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:23829357","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23829357","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.8999999761581421,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W1656114533","https://openalex.org/W1986240377","https://openalex.org/W2006420867","https://openalex.org/W2006880135","https://openalex.org/W2014490066","https://openalex.org/W2058806155","https://openalex.org/W2061259478","https://openalex.org/W2078749611","https://openalex.org/W2096914244","https://openalex.org/W2105668062","https://openalex.org/W2108508060","https://openalex.org/W2129858246","https://openalex.org/W2147421370","https://openalex.org/W2152964937","https://openalex.org/W2158534713","https://openalex.org/W2499960806","https://openalex.org/W2503171200","https://openalex.org/W4301014524"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W2078959398","https://openalex.org/W3135576859","https://openalex.org/W34328406","https://openalex.org/W1963920545"],"abstract_inverted_index":{"This":[0],"paper":[1],"is":[2,28,75],"devoted":[3],"to":[4,83,176],"results":[5,150],"obtained":[6],"by":[7,93],"the":[8,13,18,29,35,38,52,66,76,89,94,99,109,129,133,152,168],"docking":[9,31,116],"program":[10,15,32,117],"SOL":[11,21,27,73,118,142,163,178],"and":[12,22,59,62,103,143,164,179],"post-processing":[14],"DISCORE":[16,23,87,144,165,180],"at":[17],"CSAR":[19,140],"benchmark.":[20],"programs":[24],"are":[25,181],"described.":[26],"original":[30],"developed":[33],"on":[34,108,151],"basis":[36],"of":[37,54,85,98,111,132,139,172],"genetic":[39],"algorithm,":[40],"MMFF94":[41],"force":[42],"field,":[43],"rigid":[44],"protein,":[45],"precalculated":[46],"energy":[47,91,96,156],"grid":[48],"including":[49],"desolvation":[50],"in":[51,128,136,170],"frame":[53],"simplified":[55],"GB":[56],"model,":[57],"vdW,":[58],"electrostatic":[60],"interactions":[61],"taking":[63],"into":[64],"account":[65],"ligand":[67,100,126],"internal":[68],"strain":[69],"energy.":[70],"An":[71],"important":[72],"feature":[74],"single-":[77],"or":[78],"multi-processor":[79],"performance":[80],"for":[81,124,159],"up":[82],"hundreds":[84],"CPUs.":[86],"improves":[88],"binding":[90,154],"scoring":[92],"local":[95],"optimization":[97],"docked":[101],"pose":[102],"a":[104,121],"simple":[105],"linear":[106],"regression":[107],"base":[110],"available":[112],"experimental":[113],"data.":[114],"The":[115],"has":[119],"demonstrated":[120,147],"good":[122],"ability":[123],"correct":[125],"positioning":[127],"active":[130],"sites":[131],"tested":[134],"proteins":[135],"most":[137],"cases":[138],"exercises.":[141],"have":[145],"not":[146],"very":[148],"exciting":[149],"protein-ligand":[153],"free":[155],"estimation.":[157],"Nevertheless,":[158],"some":[160],"target":[161],"proteins,":[162],"were":[166],"among":[167],"first":[169],"prediction":[171],"inhibition":[173],"activity.":[174],"Ways":[175],"improve":[177],"discussed.":[182]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
