{"id":"https://openalex.org/W2761273232","doi":"https://doi.org/10.1021/acs.jcim.7b00505","title":"Benchmarking Commercial Conformer Ensemble Generators","display_name":"Benchmarking Commercial Conformer Ensemble Generators","publication_year":2017,"publication_date":"2017-10-02","ids":{"openalex":"https://openalex.org/W2761273232","doi":"https://doi.org/10.1021/acs.jcim.7b00505","mag":"2761273232","pmid":"https://pubmed.ncbi.nlm.nih.gov/28967749"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00505","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00505","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/A5034544143","display_name":"Nils\u2010Ole Friedrich","orcid":"https://orcid.org/0000-0002-8983-388X"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Nils-Ole Friedrich","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034475539","display_name":"Christina de Bruyn Kops","orcid":"https://orcid.org/0000-0001-8890-2137"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christina de Bruyn Kops","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048360660","display_name":"Florian Flachsenberg","orcid":"https://orcid.org/0000-0001-7051-8719"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Florian Flachsenberg","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019475748","display_name":"Kai Sommer","orcid":"https://orcid.org/0000-0003-1866-8247"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Kai Sommer","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083205378","display_name":"Matthias Rarey","orcid":"https://orcid.org/0000-0002-9553-6531"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Rarey","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065353728","display_name":"Johannes Kirchmair","orcid":"https://orcid.org/0000-0003-2667-5877"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Johannes Kirchmair","raw_affiliation_strings":["Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, Universit\u00e4t Hamburg, Bundesstr. 43, Hamburg 20146, Germany","institution_ids":["https://openalex.org/I159176309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5034544143"],"corresponding_institution_ids":["https://openalex.org/I159176309"],"apc_list":null,"apc_paid":null,"fwci":10.8996,"has_fulltext":false,"cited_by_count":131,"citation_normalized_percentile":{"value":0.98866044,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"57","issue":"11","first_page":"2719","last_page":"2728"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9959999918937683,"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"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9927999973297119,"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/conformational-isomerism","display_name":"Conformational isomerism","score":0.8762966394424438},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7058756947517395},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5663635730743408},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.551720917224884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46316349506378174},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.338974267244339},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25545793771743774},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.21679410338401794}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.8762966394424438},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7058756947517395},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5663635730743408},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.551720917224884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46316349506378174},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.338974267244339},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25545793771743774},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.21679410338401794},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.7b00505","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00505","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:28967749","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28967749","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":28,"referenced_works":["https://openalex.org/W1976848779","https://openalex.org/W1995850373","https://openalex.org/W1998000033","https://openalex.org/W2010099233","https://openalex.org/W2013083986","https://openalex.org/W2020429677","https://openalex.org/W2038840577","https://openalex.org/W2069010397","https://openalex.org/W2070405735","https://openalex.org/W2071579644","https://openalex.org/W2072537419","https://openalex.org/W2078145018","https://openalex.org/W2078374001","https://openalex.org/W2085822586","https://openalex.org/W2100125011","https://openalex.org/W2121044470","https://openalex.org/W2127463492","https://openalex.org/W2127790232","https://openalex.org/W2130479394","https://openalex.org/W2147421370","https://openalex.org/W2152903006","https://openalex.org/W2158219301","https://openalex.org/W2208203352","https://openalex.org/W2222589778","https://openalex.org/W2244785476","https://openalex.org/W2587816047","https://openalex.org/W2726184500","https://openalex.org/W2763443264"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967"],"abstract_inverted_index":{"2017,":[0],"57,":[1],"529-539).":[2],"For":[3],"commercial":[4,88],"algorithms,":[5],"the":[6,86],"median":[7],"minimum":[8],"root-mean-square":[9],"deviations":[10],"measured":[11],"between":[12,25],"protein-bound":[13],"ligand":[14],"conformations":[15],"and":[16,27,50,102],"ensembles":[17],"of":[18,21,44,85],"a":[19,74,92],"maximum":[20],"250":[22],"conformers":[23],"are":[24,34],"0.46":[26],"0.61":[28],"\u00c5.":[29],"Commercial":[30],"conformer":[31],"ensemble":[32],"generators":[33],"characterized":[35],"by":[36],"their":[37,60],"high":[38],"robustness,":[39],"with":[40],"at":[41],"least":[42],"99%":[43],"all":[45],"input":[46],"molecules":[47],"successfully":[48],"processed":[49],"few":[51],"or":[52],"even":[53],"no":[54],"substantial":[55],"geometrical":[56],"errors":[57],"detectable":[58],"in":[59,110],"output":[61],"conformations.":[62],"The":[63],"RDKit":[64],"distance":[65],"geometry":[66],"algorithm":[67],"(with":[68],"minimization":[69],"enabled)":[70],"appears":[71],"to":[72,83,100,104],"be":[73],"good":[75],"free":[76],"alternative":[77],"since":[78],"its":[79],"performance":[80,109],"is":[81],"comparable":[82],"that":[84],"midranked":[87],"algorithms.":[89],"Based":[90],"on":[91,97],"statistical":[93],"analysis,":[94],"we":[95],"elaborate":[96],"which":[98],"algorithms":[99],"use":[101],"how":[103],"parametrize":[105],"them":[106],"for":[107],"best":[108],"different":[111],"application":[112],"scenarios.":[113]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":23},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":22},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":13}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}