{"id":"https://openalex.org/W2244785476","doi":"https://doi.org/10.1021/acs.jcim.5b00654","title":"Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation","display_name":"Better Informed Distance Geometry: Using What We Know To Improve Conformation Generation","publication_year":2015,"publication_date":"2015-11-17","ids":{"openalex":"https://openalex.org/W2244785476","doi":"https://doi.org/10.1021/acs.jcim.5b00654","mag":"2244785476","pmid":"https://pubmed.ncbi.nlm.nih.gov/26575315"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00654","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00654","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/A5019754904","display_name":"Sereina Riniker","orcid":"https://orcid.org/0000-0003-1893-4031"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Sereina Riniker","raw_affiliation_strings":["Laboratory of Physical Chemistry, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093 Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratory of Physical Chemistry, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093 Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056808182","display_name":"Gregory A. Landrum","orcid":"https://orcid.org/0000-0001-6279-4481"},"institutions":[{"id":"https://openalex.org/I1283582996","display_name":"Novartis (Switzerland)","ror":"https://ror.org/02f9zrr09","country_code":"CH","type":"company","lineage":["https://openalex.org/I1283582996"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gregory A. Landrum","raw_affiliation_strings":["Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland"],"affiliations":[{"raw_affiliation_string":"Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I1283582996"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019754904"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":null,"apc_paid":null,"fwci":12.3695,"has_fulltext":false,"cited_by_count":716,"citation_normalized_percentile":{"value":0.9901161,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"55","issue":"12","first_page":"2562","last_page":"2574"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9958999752998352,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9944000244140625,"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":0.7088288068771362},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.5644572377204895},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.5485889315605164},{"id":"https://openalex.org/keywords/molecular-geometry","display_name":"Molecular geometry","score":0.5463807582855225},{"id":"https://openalex.org/keywords/ideal","display_name":"Ideal (ethics)","score":0.5286173224449158},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.4911915957927704},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.48549726605415344},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4598134458065033},{"id":"https://openalex.org/keywords/bond-length","display_name":"Bond length","score":0.4559394419193268},{"id":"https://openalex.org/keywords/torsion","display_name":"Torsion (gastropod)","score":0.44983890652656555},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4225514233112335},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3489341139793396},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3238658905029297},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3128480911254883},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.266614705324173},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18469613790512085},{"id":"https://openalex.org/keywords/mathematical-analysis","display_name":"Mathematical analysis","score":0.11031734943389893},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.10945898294448853}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.7088288068771362},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5644572377204895},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.5485889315605164},{"id":"https://openalex.org/C193547582","wikidata":"https://www.wikidata.org/wiki/Q911331","display_name":"Molecular geometry","level":3,"score":0.5463807582855225},{"id":"https://openalex.org/C2776639384","wikidata":"https://www.wikidata.org/wiki/Q840396","display_name":"Ideal (ethics)","level":2,"score":0.5286173224449158},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.4911915957927704},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.48549726605415344},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4598134458065033},{"id":"https://openalex.org/C155860418","wikidata":"https://www.wikidata.org/wiki/Q863695","display_name":"Bond length","level":3,"score":0.4559394419193268},{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.44983890652656555},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4225514233112335},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3489341139793396},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3238658905029297},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3128480911254883},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.266614705324173},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18469613790512085},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.11031734943389893},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10945898294448853},{"id":"https://openalex.org/C141071460","wikidata":"https://www.wikidata.org/wiki/Q40821","display_name":"Surgery","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":false},{"descriptor_ui":"D009930","descriptor_name":"Organic Chemicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009930","descriptor_name":"Organic Chemicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D009930","descriptor_name":"Organic Chemicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00654","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00654","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:26575315","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26575315","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":[{"display_name":"Affordable and clean energy","score":0.6399999856948853,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1522205938","https://openalex.org/W1967689294","https://openalex.org/W1969585025","https://openalex.org/W1976848779","https://openalex.org/W1983194490","https://openalex.org/W1988037271","https://openalex.org/W1995850373","https://openalex.org/W2001428495","https://openalex.org/W2011092162","https://openalex.org/W2014123957","https://openalex.org/W2024610405","https://openalex.org/W2030971064","https://openalex.org/W2032842297","https://openalex.org/W2038361288","https://openalex.org/W2047509756","https://openalex.org/W2052818547","https://openalex.org/W2072537419","https://openalex.org/W2077467665","https://openalex.org/W2078374001","https://openalex.org/W2094278785","https://openalex.org/W2100125011","https://openalex.org/W2107790922","https://openalex.org/W2121853844","https://openalex.org/W2127463492","https://openalex.org/W2127790232","https://openalex.org/W2130479394","https://openalex.org/W2147122257","https://openalex.org/W2147421370","https://openalex.org/W2148950790","https://openalex.org/W2152903006","https://openalex.org/W2154212025","https://openalex.org/W2200866600","https://openalex.org/W2204230050","https://openalex.org/W6912406780"],"related_works":["https://openalex.org/W2148970764","https://openalex.org/W2011402683","https://openalex.org/W1983148835","https://openalex.org/W2620453713","https://openalex.org/W2039508568","https://openalex.org/W2962752589","https://openalex.org/W2044744623","https://openalex.org/W2012102807","https://openalex.org/W2005280937","https://openalex.org/W1964334027"],"abstract_inverted_index":{"Small":[0],"organic":[1],"molecules":[2,57,263],"are":[3,28,176,213],"often":[4,177],"flexible,":[5],"i.e.,":[6,128],"they":[7],"can":[8,80],"adopt":[9],"a":[10,59,76,120,136,144,180,216],"variety":[11],"of":[12,62,75,93,105,123,220,245,261],"low-energy":[13],"conformations":[14,175,255],"in":[15,19,50,230],"solution":[16],"that":[17,156,195],"exist":[18],"equilibrium":[20],"with":[21,58,179,201],"each":[22,44],"other.":[23],"Two":[24],"main":[25],"search":[26],"strategies":[27],"used":[29],"to":[30,56,84,148,161,163,252],"generate":[31,149],"representative":[32],"conformational":[33,73],"ensembles":[34],"for":[35,96],"molecules:":[36],"systematic":[37],"and":[38,79,108,135,167,186,236,249,264],"stochastic.":[39],"In":[40,111],"the":[41,68,72,112,117,154,173,197,231,243,246,250,258],"first":[42],"approach,":[43,115],"rotatable":[45,63],"bond":[46,130,133],"is":[47,126,143,228,239],"sampled":[48],"systematically":[49],"discrete":[51],"intervals,":[52],"limiting":[53],"its":[54,237],"use":[55,102],"small":[60,262],"number":[61],"bonds.":[64],"Stochastic":[65],"methods,":[66],"on":[67,116],"other":[69,118],"hand,":[70,119],"sample":[71],"space":[74],"molecule":[77],"randomly":[78],"thus":[81],"be":[82],"applied":[83],"more":[85],"flexible":[86],"molecules.":[87],"Different":[88],"methods":[89,101],"employ":[90],"different":[91],"degrees":[92],"experimental":[94,202],"data":[95],"conformer":[97],"generation.":[98],"So-called":[99],"knowledge-based":[100],"predefined":[103],"libraries":[104],"torsional":[106,139,211],"angles":[107,212],"ring":[109],"conformations.":[110],"distance":[113,198],"geometry":[114,142,199],"smaller":[121],"amount":[122],"empirical":[124],"information":[125],"used,":[127],"ideal":[129,132,138],"lengths,":[131],"angles,":[134],"few":[137],"angles.":[140],"Distance":[141],"computationally":[145],"fast":[146],"method":[147],"conformers,":[150],"but":[151],"it":[152],"has":[153],"downside":[155],"purely":[157],"distance-based":[158],"constraints":[159],"tend":[160],"lead":[162],"distorted":[164],"aromatic":[165],"rings":[166],"sp(2)":[168],"centers.":[169],"To":[170],"correct":[171],"this,":[172],"resulting":[174],"minimized":[178],"force":[181],"field,":[182],"adding":[183],"computational":[184],"complexity":[185],"run":[187],"time.":[188],"Here":[189],"we":[190],"present":[191],"an":[192],"alternative":[193],"strategy":[194],"combines":[196],"approach":[200,227],"torsion-angle":[203],"preferences":[204],"obtained":[205],"from":[206,257],"small-molecule":[207],"crystallographic":[208],"data.":[209],"The":[210,225],"described":[214],"by":[215,241],"previously":[217],"developed":[218],"set":[219],"hierarchically":[221],"structured":[222],"SMARTS":[223],"patterns.":[224],"new":[226],"implemented":[229],"open-source":[232],"cheminformatics":[233],"library":[234],"RDKit,":[235],"performance":[238],"assessed":[240],"comparing":[242],"diversity":[244],"generated":[247],"ensemble":[248],"ability":[251],"reproduce":[253],"crystal":[254,259],"taken":[256],"structures":[260],"protein-ligand":[265],"complexes.":[266]},"counts_by_year":[{"year":2026,"cited_by_count":32},{"year":2025,"cited_by_count":127},{"year":2024,"cited_by_count":136},{"year":2023,"cited_by_count":119},{"year":2022,"cited_by_count":80},{"year":2021,"cited_by_count":88},{"year":2020,"cited_by_count":63},{"year":2019,"cited_by_count":37},{"year":2018,"cited_by_count":22},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":2}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
