{"id":"https://openalex.org/W2802933734","doi":"https://doi.org/10.1021/acs.jcim.8b00010","title":"Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking","display_name":"Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking","publication_year":2018,"publication_date":"2018-04-23","ids":{"openalex":"https://openalex.org/W2802933734","doi":"https://doi.org/10.1021/acs.jcim.8b00010","mag":"2802933734","pmid":"https://pubmed.ncbi.nlm.nih.gov/29683661"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00010","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_indexed_in_scopus":true,"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":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-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/A5005819437","display_name":"Claas Strecker","orcid":"https://orcid.org/0000-0003-0169-8482"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"funder","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Claas Strecker","raw_affiliation_strings":["Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103205701","display_name":"Bernd Meyer","orcid":"https://orcid.org/0000-0001-5348-3091"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"funder","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Bernd Meyer","raw_affiliation_strings":["Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103205701"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":1.212,"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":15,"citation_normalized_percentile":{"value":0.825482,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":89},"biblio":{"volume":"58","issue":"5","first_page":"1121","last_page":"1131"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9999,"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":0.9999,"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":0.9985,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9944,"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/docking","display_name":"Docking (animal)","score":0.81387997}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.81387997},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5394171},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5306712},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.49970555},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.48972988},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3800316},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37955064},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33881593},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33245897},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.20928878},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10706407},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012083","descriptor_name":"Renin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012083","descriptor_name":"Renin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012083","descriptor_name":"Renin","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.8b00010","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_indexed_in_scopus":true,"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":null,"is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29683661","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_indexed_in_scopus":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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":null,"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":44,"referenced_works":["https://openalex.org/W1968319881","https://openalex.org/W1970208561","https://openalex.org/W1974422922","https://openalex.org/W1984030577","https://openalex.org/W1990137109","https://openalex.org/W1990755847","https://openalex.org/W2003127541","https://openalex.org/W2005445463","https://openalex.org/W2008518939","https://openalex.org/W2015367396","https://openalex.org/W2038542598","https://openalex.org/W2039526577","https://openalex.org/W2042110087","https://openalex.org/W2061799302","https://openalex.org/W2066517589","https://openalex.org/W2066620494","https://openalex.org/W2067074955","https://openalex.org/W2067093847","https://openalex.org/W2067216438","https://openalex.org/W2079153029","https://openalex.org/W2084485490","https://openalex.org/W2088215785","https://openalex.org/W2092693813","https://openalex.org/W2102174621","https://openalex.org/W2107914594","https://openalex.org/W2114819818","https://openalex.org/W2134312057","https://openalex.org/W2141603742","https://openalex.org/W2143729668","https://openalex.org/W2145722722","https://openalex.org/W2149620192","https://openalex.org/W2152825437","https://openalex.org/W2161134038","https://openalex.org/W2163915395","https://openalex.org/W2165779834","https://openalex.org/W2171146813","https://openalex.org/W2210796249","https://openalex.org/W2328207411","https://openalex.org/W2346710580","https://openalex.org/W2399536524","https://openalex.org/W2520833569","https://openalex.org/W2522254499","https://openalex.org/W4210388672","https://openalex.org/W4242587876"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W2773493604","https://openalex.org/W2750247885","https://openalex.org/W2336040088","https://openalex.org/W2269591907","https://openalex.org/W2182722930","https://openalex.org/W2093426296","https://openalex.org/W2057846043","https://openalex.org/W2038399774","https://openalex.org/W2027065525"],"abstract_inverted_index":{"Protein":[0],"flexibility":[1],"poses":[2,214],"a":[3,38,50,54,60,86,97,179],"major":[4],"challenge":[5],"to":[6,32,65,168,187,209],"docking":[7,58,114,161],"of":[8,41,44,82,105,127,138,156,202,226,233,243,252,259],"potential":[9],"ligands":[10],"in":[11,147,231,257],"that":[12],"the":[13,24,30,42,45,76,103,154,211],"binding":[14,46,142,164],"site":[15,143],"can":[16,48],"adopt":[17],"different":[18],"shapes.":[19],"Docking":[20],"algorithms":[21],"usually":[22],"keep":[23],"protein":[25,83],"rigid":[26],"and":[27,75,99,119,175,206],"only":[28],"allow":[29],"ligand":[31,51,213],"be":[33,188],"treated":[34],"as":[35,236,238],"flexible.":[36],"However,":[37],"wrong":[39],"assessment":[40],"shape":[43],"pocket":[47],"prevent":[49],"from":[52,123],"adapting":[53],"correct":[55],"pose.":[56],"Ensemble":[57],"is":[59,85,207],"simple":[61],"yet":[62],"promising":[63],"method":[64],"solve":[66],"this":[67,90,93,222],"problem:":[68],"Ligands":[69],"are":[70,78],"docked":[71],"into":[72],"multiple":[73],"structures,":[74],"results":[77],"subsequently":[79],"merged.":[80],"Selection":[81],"structures":[84,118,121,205,230,245],"significant":[87],"factor":[88],"for":[89,132,159,181],"approach.":[91],"In":[92],"work":[94],"we":[95],"perform":[96,112,246],"comprehensive":[98],"comparative":[100],"study":[101],"evaluating":[102],"impact":[104],"structure":[106,157,256],"selection":[107,158],"on":[108,247],"ensemble":[109,113,160,182,200,223],"docking.":[110],"We":[111,152],"with":[115,120,194],"several":[116],"crystal":[117,150,204,219,229,255],"derived":[122],"molecular":[124],"dynamics":[125],"simulations":[126,140],"renin,":[128],"an":[129],"attractive":[130],"target":[131],"antihypertensive":[133],"drugs.":[134],"Here,":[135],"500":[136],"ns":[137],"MD":[139],"revealed":[141],"shapes":[144],"not":[145],"found":[146],"any":[148,217,253],"available":[149],"structure.":[151,220],"evaluate":[153],"importance":[155],"by":[162],"comparing":[163],"pose":[165],"prediction,":[166],"ability":[167],"rank":[169],"actives":[170],"above":[171],"nonactives":[172],"(screening":[173],"utility),":[174],"scoring":[176,239,260],"accuracy.":[177,240],"As":[178],"result,":[180],"definition":[183],"k-means":[184],"clustering":[185,193],"appears":[186],"better":[189,215,249],"suited":[190],"than":[191,216,250],"hierarchical":[192],"average":[195,248],"linkage.":[196],"The":[197],"best":[198],"performing":[199],"consists":[201],"four":[203],"able":[208],"reproduce":[210],"native":[212],"individual":[218,228,254],"Moreover":[221],"outperforms":[224],"88%":[225],"all":[227,263],"terms":[232,258],"screening":[234],"utility":[235],"well":[237],"Similarly,":[241],"ensembles":[242,265],"MD-derived":[244],"75%":[251],"accuracy":[261],"at":[262],"inspected":[264],"sizes.":[266]},"abstract_inverted_index_v3":null,"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2802933734","counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-02-16T03:01:00.399407","created_date":"2018-05-17"}