{"id":"https://openalex.org/W2440823401","doi":"https://doi.org/10.1021/acs.jcim.5b00279","title":"Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise","display_name":"Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise","publication_year":2015,"publication_date":"2015-08-06","ids":{"openalex":"https://openalex.org/W2440823401","doi":"https://doi.org/10.1021/acs.jcim.5b00279","mag":"2440823401","pmid":"https://pubmed.ncbi.nlm.nih.gov/26247231"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00279","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00279","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/A5101839372","display_name":"Ashutosh Kumar","orcid":"https://orcid.org/0000-0002-1699-2951"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ashutosh Kumar","raw_affiliation_strings":["Structural Bioinformatics\rTeam, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics\rTeam, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044307373","display_name":"Kam Y. J. Zhang","orcid":"https://orcid.org/0000-0002-9282-8045"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kam Y. J. Zhang","raw_affiliation_strings":["Structural Bioinformatics\rTeam, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan"],"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics\rTeam, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101839372"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.9072,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.95746013,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"56","issue":"6","first_page":"965","last_page":"973"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9793000221252441,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9739000201225281,"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/virtual-screening","display_name":"Virtual screening","score":0.8974519968032837},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.6940558552742004},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5441807508468628},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5440293550491333},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5421115159988403},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5089185237884521},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.41809841990470886},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3657723665237427},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23934191465377808},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.2138725221157074},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1888023018836975},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1328253448009491}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.8974519968032837},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.6940558552742004},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5441807508468628},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5440293550491333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5421115159988403},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5089185237884521},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.41809841990470886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3657723665237427},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23934191465377808},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.2138725221157074},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1888023018836975},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1328253448009491},{"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/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","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.5b00279","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00279","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:26247231","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26247231","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":[],"funders":[{"id":"https://openalex.org/F4320335125","display_name":"RIKEN","ror":"https://ror.org/01sjwvz98"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":66,"referenced_works":["https://openalex.org/W1592950931","https://openalex.org/W1605578858","https://openalex.org/W1966041739","https://openalex.org/W1966172022","https://openalex.org/W1967026937","https://openalex.org/W1969017960","https://openalex.org/W1977467384","https://openalex.org/W1979966120","https://openalex.org/W1983143653","https://openalex.org/W1984981677","https://openalex.org/W1985588649","https://openalex.org/W1993403967","https://openalex.org/W1998568556","https://openalex.org/W1998848097","https://openalex.org/W2000825058","https://openalex.org/W2007066406","https://openalex.org/W2008732224","https://openalex.org/W2009423060","https://openalex.org/W2013085020","https://openalex.org/W2014265202","https://openalex.org/W2025251866","https://openalex.org/W2027065525","https://openalex.org/W2028609644","https://openalex.org/W2032233064","https://openalex.org/W2033882981","https://openalex.org/W2034419650","https://openalex.org/W2035395192","https://openalex.org/W2037167896","https://openalex.org/W2038150706","https://openalex.org/W2038542598","https://openalex.org/W2041189078","https://openalex.org/W2042071104","https://openalex.org/W2044303151","https://openalex.org/W2045682025","https://openalex.org/W2051381895","https://openalex.org/W2053253524","https://openalex.org/W2059230675","https://openalex.org/W2059464558","https://openalex.org/W2064789519","https://openalex.org/W2065014569","https://openalex.org/W2067732724","https://openalex.org/W2068672372","https://openalex.org/W2070880994","https://openalex.org/W2071557543","https://openalex.org/W2072886335","https://openalex.org/W2075186867","https://openalex.org/W2093876128","https://openalex.org/W2102377211","https://openalex.org/W2103581045","https://openalex.org/W2107063279","https://openalex.org/W2112213938","https://openalex.org/W2112411768","https://openalex.org/W2121776789","https://openalex.org/W2121895929","https://openalex.org/W2134967712","https://openalex.org/W2135080928","https://openalex.org/W2143419487","https://openalex.org/W2151803551","https://openalex.org/W2160205549","https://openalex.org/W2162606439","https://openalex.org/W2317062241","https://openalex.org/W2322472987","https://openalex.org/W2412446857","https://openalex.org/W2419225477","https://openalex.org/W2949243165","https://openalex.org/W4240773179"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2093426296","https://openalex.org/W2336040088","https://openalex.org/W2038399774","https://openalex.org/W2750247885"],"abstract_inverted_index":{"To":[0],"evaluate":[1],"the":[2,17,23,60,99,112,116,130,153,157,175,184,224],"applicability":[3],"of":[4,27,105,121,174,186,193,200],"shape":[5,73,89,142,187,227],"similarity":[6,74,90,143,188,228],"in":[7,16,54,124,179],"docking-based":[8,77,194],"pose":[9,26,78,101,114,118,131,162],"selection":[10,79,132],"and":[11,35,52,80,145,170,196,206],"virtual":[12,81,154,190],"screening,":[13],"we":[14,64],"participated":[15],"CSARdock2014":[18,61,180],"benchmark":[19,62,181],"exercise":[20,39],"for":[21,44,119,160,209],"identifying":[22],"correct":[24],"docking":[25,49,207],"inhibitors":[28,214],"targeting":[29],"factor":[30],"XA,":[31],"spleen":[32,211],"tyrosine":[33,212],"kinase,":[34],"tRNA":[36],"methyltransferase.":[37],"This":[38],"provides":[40],"a":[41,55,125],"valuable":[42],"opportunity":[43],"researchers":[45],"to":[46,75,97,147,166,217],"test":[47,122],"their":[48],"programs,":[50],"methods,":[51],"protocols":[53],"blind":[56,126],"testing":[57,127],"environment.":[58,128],"In":[59,152],"exercise,":[63,156],"have":[65],"implemented":[66],"an":[67,103,136],"approach":[68],"that":[69,86],"uses":[70],"ligand":[71,87,140,225],"3D":[72,88,141,226],"facilitate":[76],"screening.":[82],"We":[83],"showed":[84],"here":[85],"between":[91,139,203],"bound":[92],"poses":[93],"could":[94],"be":[95,167,218],"used":[96],"identify":[98],"native-like":[100],"from":[102],"ensemble":[104],"docking-generated":[106],"poses.":[107],"Our":[108],"method":[109],"correctly":[110],"identified":[111],"native":[113],"as":[115],"top-ranking":[117],"73%":[120],"cases":[123],"Moreover,":[129],"results":[133],"also":[134],"revealed":[135],"excellent":[137],"correlation":[138],"scores":[144,208],"RMSD":[146,159],"X-ray":[148],"crystal":[149],"structure":[150],"ligand.":[151],"screening":[155,191],"average":[158],"our":[161],"prediction":[163],"was":[164,172,215,229],"found":[165,216],"1.02":[168],"\u00c5,":[169],"it":[171],"one":[173],"top":[176],"performances":[177],"achieved":[178],"exercise.":[182],"Furthermore,":[183],"inclusion":[185],"improved":[189],"performance":[192],"scoring":[195],"ranking.":[197],"The":[198],"coefficient":[199],"determination":[201],"(r(2))":[202],"experimental":[204],"activities":[205],"276":[210],"kinase":[213],"0.365":[219],"but":[220],"reached":[221],"0.614":[222],"when":[223],"included.":[230]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}