{"id":"https://openalex.org/W2315317366","doi":"https://doi.org/10.1021/jp2120143","title":"Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses","display_name":"Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses","publication_year":2012,"publication_date":"2012-04-10","ids":{"openalex":"https://openalex.org/W2315317366","doi":"https://doi.org/10.1021/jp2120143","mag":"2315317366","pmid":"https://pubmed.ncbi.nlm.nih.gov/22490366"},"language":"en","primary_location":{"id":"doi:10.1021/jp2120143","doi":"https://doi.org/10.1021/jp2120143","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp2120143","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},"volume":null,"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/A5054127002","display_name":"Michael T. Zimmermann","orcid":"https://orcid.org/0000-0001-7073-0525","observed_orcids":["https://orcid.org/0000-0001-7073-0525"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael T. Zimmermann","raw_affiliation_strings":["Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072961886","display_name":"Sumudu P. Leelananda","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumudu P. Leelananda","raw_affiliation_strings":["Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086880109","display_name":"Andrzej Kloczkowski","orcid":"https://orcid.org/0000-0003-1002-5095","observed_orcids":["https://orcid.org/0000-0003-1002-5095"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrzej Kloczkowski","raw_affiliation_strings":["Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States","institution_ids":["https://openalex.org/I173911158"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023494109","display_name":"Robert L. Jernigan","orcid":"https://orcid.org/0000-0003-0996-8360","observed_orcids":["https://orcid.org/0000-0003-0996-8360"]},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert L. Jernigan","raw_affiliation_strings":["Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics\rand Computational Biology Interdepartmental Graduate Program, \u2021Department of Biochemistry,\rBiophysics, and Molecular Biology, and \u00a7LH Baker Center of Bioinformatics and Biological\rStatistics, Iowa State University, Ames, Iowa 50011, United States","institution_ids":["https://openalex.org/I173911158"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023494109"],"corresponding_institution_ids":["https://openalex.org/I173911158"],"apc_list":null,"apc_paid":null,"fwci":1.0831,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.75485441,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"116","issue":"23","first_page":"6725","last_page":"6731"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9970999956130981,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9970999956130981,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0017000000225380063,"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/T11162","display_name":"Enzyme Structure and Function","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"protein structure prediction","score":0.6740000247955322},{"id":"https://openalex.org/keywords/protein-protein-docking","display_name":"protein-protein docking","score":0.9950000047683716},{"id":"https://openalex.org/keywords/structure-evaluation","display_name":"structure evaluation","score":0.640999972820282}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7228139042854309},{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.6286917328834534},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5555357933044434},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38349542021751404},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35734719038009644},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.32297855615615845},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19481006264686584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1705552339553833},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.07029291987419128},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/jp2120143","doi":"https://doi.org/10.1021/jp2120143","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jp2120143","pdf_url":null,"source":{"id":"https://openalex.org/S185621672","display_name":"The Journal of Physical Chemistry B","issn_l":"1520-5207","issn":["1520-5207","1520-6106"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-140","russia-white-list-2","vabb-shw"],"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":"The Journal of Physical Chemistry B","raw_type":"journal-article"},{"id":"pmid:22490366","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22490366","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,"listed_in":[],"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":"The journal of physical chemistry. B","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W15000766","https://openalex.org/W1589812083","https://openalex.org/W1595256727","https://openalex.org/W1975017420","https://openalex.org/W1996869032","https://openalex.org/W1998643862","https://openalex.org/W2005696873","https://openalex.org/W2013309178","https://openalex.org/W2017807075","https://openalex.org/W2018840610","https://openalex.org/W2022488335","https://openalex.org/W2030603945","https://openalex.org/W2035376403","https://openalex.org/W2036234596","https://openalex.org/W2037928576","https://openalex.org/W2045777307","https://openalex.org/W2051291224","https://openalex.org/W2058001460","https://openalex.org/W2059508494","https://openalex.org/W2074104861","https://openalex.org/W2078688023","https://openalex.org/W2086851494","https://openalex.org/W2091778154","https://openalex.org/W2095509648","https://openalex.org/W2096339761","https://openalex.org/W2101017457","https://openalex.org/W2103717543","https://openalex.org/W2109610280","https://openalex.org/W2112743424","https://openalex.org/W2116743097","https://openalex.org/W2117515038","https://openalex.org/W2118514515","https://openalex.org/W2120513776","https://openalex.org/W2121150070","https://openalex.org/W2124146693","https://openalex.org/W2124981562","https://openalex.org/W2125677968","https://openalex.org/W2129414710","https://openalex.org/W2133712572","https://openalex.org/W2135395577","https://openalex.org/W2137736208","https://openalex.org/W2145009293","https://openalex.org/W2148645951","https://openalex.org/W2150399099","https://openalex.org/W2152195021","https://openalex.org/W2153613893","https://openalex.org/W2161776897","https://openalex.org/W2162682281","https://openalex.org/W2165271176","https://openalex.org/W2171249995","https://openalex.org/W2171546617","https://openalex.org/W2221054388","https://openalex.org/W2341285941","https://openalex.org/W4245892713"],"related_works":["https://openalex.org/W1980325697","https://openalex.org/W1999613945","https://openalex.org/W2074002527","https://openalex.org/W88781131","https://openalex.org/W2152284999","https://openalex.org/W2006054981","https://openalex.org/W2763832915","https://openalex.org/W7097518400","https://openalex.org/W2051291224","https://openalex.org/W2076022581"],"abstract_inverted_index":{"Protein":[0],"structure":[1,22,49,59,83],"prediction":[2,50],"and":[3,8,51,139,149,152],"protein-protein":[4],"docking":[5,125,133,173],"are":[6,37,77,86,155],"important":[7],"widely":[9],"used":[10,145],"tools,":[11],"but":[12,169],"methods":[13,85],"to":[14,39,62,67,82,114],"confidently":[15],"evaluate":[16,40],"the":[17,56,64,68,109,136,178],"quality":[18,172],"of":[19,43,117,132],"a":[20,41],"predicted":[21,44],"or":[23,33],"binding":[24],"pose":[25],"have":[26],"had":[27],"limited":[28],"success.":[29],"Typically,":[30],"either":[31],"knowledge-based":[32],"physics-based":[34],"energy":[35,58],"functions":[36],"employed":[38],"set":[42],"structures":[45,119],"(termed":[46],"\"decoys\"":[47],"in":[48,53],"\"poses\"":[52],"docking),":[54],"with":[55,99],"lowest":[57],"being":[60],"assumed":[61],"be":[63],"one":[65],"closest":[66],"native":[69],"state.":[70],"While":[71],"successful":[72],"for":[73,88,120,157,170],"many":[74],"cases,":[75],"failures":[76],"still":[78],"common.":[79],"Thus,":[80],"improvements":[81],"evaluation":[84],"essential":[87],"future":[89],"improvements.":[90],"In":[91],"this":[92,163],"work,":[93],"we":[94,175],"combine":[95],"multibody":[96],"statistical":[97],"potentials":[98],"dynamics":[100],"models,":[101],"evaluating":[102],"fluctuation-based":[103],"entropies":[104],"that":[105],"include":[106,146],"contributions":[107],"from":[108,135],"entire":[110],"structure.":[111],"This":[112],"leads":[113],"enhanced":[115],"selection":[116],"native-like":[118],"CASP9":[121],"decoys,":[122],"refined":[123],"ClusPro":[124],"poses,":[126,174],"as":[127,129],"well":[128],"large":[130],"sets":[131],"poses":[134],"Benchmark":[137],"3.0":[138],"Dockground":[140],"data":[141,144],"sets.":[142],"The":[143],"both":[147],"bound":[148],"unbound":[150],"docking,":[151],"positive":[153],"results":[154],"found":[156],"each":[158],"type.":[159],"Not":[160],"only":[161],"does":[162],"method":[164],"yield":[165],"improved":[166],"average":[167],"results,":[168],"high":[171],"often":[176],"pick":[177],"best":[179],"pose.":[180]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}
