{"id":"https://openalex.org/W2086679514","doi":"https://doi.org/10.1021/ci5001086","title":"The Application of Statistical Methods to Cognate Docking: A Path Forward?","display_name":"The Application of Statistical Methods to Cognate Docking: A Path Forward?","publication_year":2014,"publication_date":"2014-04-28","ids":{"openalex":"https://openalex.org/W2086679514","doi":"https://doi.org/10.1021/ci5001086","mag":"2086679514","pmid":"https://pubmed.ncbi.nlm.nih.gov/24773409"},"language":"en","primary_location":{"id":"doi:10.1021/ci5001086","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5001086","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/A5033311640","display_name":"Paul C. D. Hawkins","orcid":"https://orcid.org/0000-0001-9715-5049"},"institutions":[{"id":"https://openalex.org/I4210158493","display_name":"Open Source Science Project","ror":"https://ror.org/0523sbv14","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210158493"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paul C. D. Hawkins","raw_affiliation_strings":["OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States"],"affiliations":[{"raw_affiliation_string":"OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":["https://openalex.org/I4210158493"]},{"raw_affiliation_string":"OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090182413","display_name":"Brian Kelley","orcid":"https://orcid.org/0000-0001-6356-7133"},"institutions":[{"id":"https://openalex.org/I4210158493","display_name":"Open Source Science Project","ror":"https://ror.org/0523sbv14","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210158493"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian P. Kelley","raw_affiliation_strings":["OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States"],"affiliations":[{"raw_affiliation_string":"OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":["https://openalex.org/I4210158493"]},{"raw_affiliation_string":"OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057042667","display_name":"Gregory L. Warren","orcid":"https://orcid.org/0000-0003-4017-0162"},"institutions":[{"id":"https://openalex.org/I4210158493","display_name":"Open Source Science Project","ror":"https://ror.org/0523sbv14","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210158493"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gregory L. Warren","raw_affiliation_strings":["OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States"],"affiliations":[{"raw_affiliation_string":"OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":["https://openalex.org/I4210158493"]},{"raw_affiliation_string":"OpenEye Scientific Software , 9 Bisbee Court, Suite D, Santa Fe, New Mexico 87508, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033311640"],"corresponding_institution_ids":["https://openalex.org/I4210158493"],"apc_list":null,"apc_paid":null,"fwci":9.4668,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.97635962,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"54","issue":"5","first_page":"1339","last_page":"1355"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10260","display_name":"Software Engineering Research","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T10260","display_name":"Software Engineering Research","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/T12423","display_name":"Software Reliability and Analysis Research","score":0.9815000295639038,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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/T10906","display_name":"AI-based Problem Solving and Planning","score":0.9732000231742859,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7515484094619751},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.558539092540741},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4992821216583252},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48356005549430847},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4570976793766022},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.44298285245895386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4413626194000244},{"id":"https://openalex.org/keywords/test-suite","display_name":"Test suite","score":0.44029465317726135},{"id":"https://openalex.org/keywords/test-case","display_name":"Test case","score":0.2596738338470459},{"id":"https://openalex.org/keywords/regression-analysis","display_name":"Regression analysis","score":0.12547385692596436}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7515484094619751},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.558539092540741},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4992821216583252},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48356005549430847},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4570976793766022},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.44298285245895386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4413626194000244},{"id":"https://openalex.org/C151552104","wikidata":"https://www.wikidata.org/wiki/Q7705809","display_name":"Test suite","level":4,"score":0.44029465317726135},{"id":"https://openalex.org/C128942645","wikidata":"https://www.wikidata.org/wiki/Q1568346","display_name":"Test case","level":3,"score":0.2596738338470459},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.12547385692596436},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004583","descriptor_name":"Electrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci5001086","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5001086","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:24773409","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24773409","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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W39572901","https://openalex.org/W1624867846","https://openalex.org/W1974734322","https://openalex.org/W1975570414","https://openalex.org/W1978171318","https://openalex.org/W1980069772","https://openalex.org/W1983194490","https://openalex.org/W1986568494","https://openalex.org/W1987205443","https://openalex.org/W1988744515","https://openalex.org/W1995952752","https://openalex.org/W1998000033","https://openalex.org/W2001191780","https://openalex.org/W2013083986","https://openalex.org/W2018989832","https://openalex.org/W2020040806","https://openalex.org/W2026198545","https://openalex.org/W2027065525","https://openalex.org/W2043855224","https://openalex.org/W2051060071","https://openalex.org/W2055410316","https://openalex.org/W2056258481","https://openalex.org/W2058433776","https://openalex.org/W2059457452","https://openalex.org/W2061583504","https://openalex.org/W2068672372","https://openalex.org/W2069523442","https://openalex.org/W2074466695","https://openalex.org/W2076419401","https://openalex.org/W2078374001","https://openalex.org/W2079159737","https://openalex.org/W2084413241","https://openalex.org/W2087484885","https://openalex.org/W2088960431","https://openalex.org/W2089447985","https://openalex.org/W2090431249","https://openalex.org/W2093426296","https://openalex.org/W2100678718","https://openalex.org/W2112101018","https://openalex.org/W2117254509","https://openalex.org/W2126728600","https://openalex.org/W2131639373","https://openalex.org/W2137139046","https://openalex.org/W2152040212","https://openalex.org/W2167073106","https://openalex.org/W2167901867","https://openalex.org/W2168941972","https://openalex.org/W2799873608","https://openalex.org/W4206316875","https://openalex.org/W4232383088","https://openalex.org/W4234386980","https://openalex.org/W4242094059","https://openalex.org/W4252684946","https://openalex.org/W4300870773"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W1511772879","https://openalex.org/W4379115841","https://openalex.org/W4200340037","https://openalex.org/W608917066","https://openalex.org/W4283652261","https://openalex.org/W1485837041","https://openalex.org/W3204955359"],"abstract_inverted_index":{"Cognate":[0],"docking":[1,13,28,35,48],"has":[2],"been":[3],"used":[4],"as":[5,121,123],"a":[6,22,39,94],"test":[7],"for":[8,15,97,183],"pose":[9,64],"prediction":[10],"quality":[11],"in":[12,32,78,117,130,148,159,169],"engines":[14],"decades.":[16],"In":[17],"this":[18,90,152],"paper,":[19],"we":[20,92],"report":[21],"statistically":[23],"rigorous":[24],"analysis":[25,99],"of":[26,41,45,59,61,74,126,137,141,146,151,186],"cognate":[27,47],"performance":[29,118],"using":[30],"tools":[31],"the":[33,46,62,66,75,79,124,181],"OpenEye":[34],"suite.":[36],"We":[37,133],"address":[38],"number":[40],"critically":[42],"important":[43],"aspects":[44],"problem":[49],"that":[50,100,135],"are":[51],"often":[52],"handled":[53],"poorly:":[54],"data":[55,70,98],"set":[56],"quality,":[57],"methods":[58,120],"comparison":[60,87],"predicted":[63],"to":[65],"experimental":[67],"pose,":[68],"and":[69,139,177],"analysis.":[71],"The":[72],"focus":[73],"paper":[76],"lies":[77],"third":[80],"problem,":[81],"extracting":[82],"maximally":[83],"predictive":[84],"knowledge":[85],"from":[86],"data.":[88],"To":[89],"end,":[91],"present":[93],"multistage":[95],"protocol":[96,173],"by":[101],"combining":[102],"classical":[103],"null-hypothesis":[104],"significance":[105],"testing":[106],"with":[107,154],"effect":[108,160],"size":[109,161],"estimation":[110,162],"provides":[111],"crucial":[112],"information":[113],"about":[114],"quantitative":[115],"differences":[116,129],"between":[119],"well":[122],"probability":[125],"finding":[127],"such":[128],"future":[131],"experiments.":[132],"suggest":[134],"developers":[136,164],"software":[138,142],"users":[140,155],"have":[143],"different":[144,149,188],"levels":[145],"interest":[147],"parts":[150],"protocol,":[153],"being":[156],"primarily":[157],"interested":[158,168],"while":[163],"may":[165],"be":[166],"most":[167],"statistical":[170],"significance.":[171],"This":[172],"is":[174],"completely":[175],"general":[176],"therefore":[178],"will":[179],"provide":[180],"basis":[182],"method":[184],"comparisons":[185],"many":[187],"kinds.":[189]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
