{"id":"https://openalex.org/W2220825152","doi":"https://doi.org/10.1021/acs.jcim.5b00522","title":"Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules","display_name":"Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules","publication_year":2015,"publication_date":"2015-12-17","ids":{"openalex":"https://openalex.org/W2220825152","doi":"https://doi.org/10.1021/acs.jcim.5b00522","mag":"2220825152","pmid":"https://pubmed.ncbi.nlm.nih.gov/26679290"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00522","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00522","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/A5021939092","display_name":"Wolfgang Guba","orcid":"https://orcid.org/0000-0002-3285-5957"},"institutions":[{"id":"https://openalex.org/I118019719","display_name":"Roche (Switzerland)","ror":"https://ror.org/00by1q217","country_code":"CH","type":"company","lineage":["https://openalex.org/I118019719"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Wolfgang Guba","raw_affiliation_strings":["Molecular\rDesign and Chemical Biology, Roche Pharma Research and Early Development\r(pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland"],"affiliations":[{"raw_affiliation_string":"Molecular\rDesign and Chemical Biology, Roche Pharma Research and Early Development\r(pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland","institution_ids":["https://openalex.org/I118019719"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003179071","display_name":"Agnes Meyder","orcid":"https://orcid.org/0000-0001-8519-5780"},"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":"Agnes Meyder","raw_affiliation_strings":["Center\rfor Bioinformatics, University of Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Center\rfor Bioinformatics, University of Hamburg, Bundesstrasse 43, D-20146 Hamburg, 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\rfor Bioinformatics, University of Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany"],"affiliations":[{"raw_affiliation_string":"Center\rfor Bioinformatics, University of Hamburg, Bundesstrasse 43, D-20146 Hamburg, Germany","institution_ids":["https://openalex.org/I159176309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031106070","display_name":"J\u00e9r\u00f4me Hert","orcid":"https://orcid.org/0000-0003-3062-8029"},"institutions":[{"id":"https://openalex.org/I118019719","display_name":"Roche (Switzerland)","ror":"https://ror.org/00by1q217","country_code":"CH","type":"company","lineage":["https://openalex.org/I118019719"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"J\u00e9r\u00f4me Hert","raw_affiliation_strings":["Molecular\rDesign and Chemical Biology, Roche Pharma Research and Early Development\r(pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland"],"affiliations":[{"raw_affiliation_string":"Molecular\rDesign and Chemical Biology, Roche Pharma Research and Early Development\r(pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland","institution_ids":["https://openalex.org/I118019719"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021939092"],"corresponding_institution_ids":["https://openalex.org/I118019719"],"apc_list":null,"apc_paid":null,"fwci":1.685,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.83723814,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"56","issue":"1","first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9983000159263611,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9983000159263611,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9966999888420105,"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":0.9966999888420105,"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/torsion","display_name":"Torsion (gastropod)","score":0.8239718675613403},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.6531182527542114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6020716428756714},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5309885144233704},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5189154148101807},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4597603976726532},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37252169847488403},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3548080325126648},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.31785643100738525},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23619866371154785},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.21518564224243164},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.11934313178062439},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11472764611244202}],"concepts":[{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.8239718675613403},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.6531182527542114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6020716428756714},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5309885144233704},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5189154148101807},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4597603976726532},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37252169847488403},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3548080325126648},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.31785643100738525},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23619866371154785},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.21518564224243164},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.11934313178062439},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11472764611244202},{"id":"https://openalex.org/C90856448","wikidata":"https://www.wikidata.org/wiki/Q431","display_name":"Zoology","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}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00522","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00522","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:26679290","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26679290","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":[{"id":"https://openalex.org/G2910151125","display_name":null,"funder_award_id":"031A183B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1973056533","https://openalex.org/W1999820454","https://openalex.org/W2001428495","https://openalex.org/W2032842297","https://openalex.org/W2095026430","https://openalex.org/W2127790232","https://openalex.org/W2130479394","https://openalex.org/W2180271118"],"related_works":["https://openalex.org/W2165912799","https://openalex.org/W2735662278","https://openalex.org/W2382615723","https://openalex.org/W4311804456","https://openalex.org/W1987484445","https://openalex.org/W2623658258","https://openalex.org/W2143413548","https://openalex.org/W1969219540","https://openalex.org/W2370459448","https://openalex.org/W2105067402"],"abstract_inverted_index":{"The":[0,28,91],"Torsion":[1],"Library":[2],"contains":[3],"hundreds":[4],"of":[5,63,94,112,120],"rules":[6,30,52],"for":[7,66,97],"small":[8,68],"molecule":[9,69],"conformations":[10,58],"which":[11],"have":[12,47],"been":[13],"derived":[14],"from":[15],"the":[16,61,116],"Cambridge":[17],"Structural":[18],"Database":[19],"(CSD)":[20],"and":[21,36,59,84,88],"are":[22,31,139],"curated":[23],"by":[24,109,133],"molecular":[25],"design":[26],"experts.":[27],"torsion":[29,51,82],"encoded":[32],"as":[33],"SMARTS":[34],"patterns":[35,83],"categorize":[37],"rotatable":[38],"bonds":[39],"via":[40],"a":[41,98,110,134],"traffic":[42],"light":[43],"coloring":[44],"scheme.":[45],"We":[46],"systematically":[48],"revised":[49],"all":[50,86],"to":[53,115],"better":[54],"identify":[55],"highly":[56],"strained":[57],"minimize":[60],"number":[62,93],"false":[64],"alerts":[65,96],"CSD":[67,100],"X-ray":[70],"structures.":[71],"For":[72],"this":[73],"new":[74],"release,":[75],"we":[76],"added":[77],"or":[78],"substantially":[79],"modified":[80],"78":[81],"reviewed":[85],"angles":[87],"tolerance":[89],"intervals.":[90],"overall":[92],"red":[95],"filtered":[99],"data":[101],"set":[102],"with":[103],"130":[104],"000":[105],"structures":[106],"was":[107],"reduced":[108],"factor":[111],"4":[113],"compared":[114],"predecessor.":[117],"This":[118],"is":[119],"clear":[121],"advantage":[122],"in":[123,140],"3D":[124],"virtual":[125],"screening":[126],"where":[127],"hits":[128],"should":[129],"only":[130],"be":[131],"removed":[132],"conformational":[135],"filter":[136],"if":[137],"they":[138],"energetically":[141],"inaccessible":[142],"conformations.":[143]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":1}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}