{"id":"https://openalex.org/W2947658954","doi":"https://doi.org/10.1186/s13321-019-0354-7","title":"Bayesian optimization for conformer generation","display_name":"Bayesian optimization for conformer generation","publication_year":2019,"publication_date":"2019-05-21","ids":{"openalex":"https://openalex.org/W2947658954","doi":"https://doi.org/10.1186/s13321-019-0354-7","mag":"2947658954","pmid":"https://pubmed.ncbi.nlm.nih.gov/31115707"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-019-0354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0354-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0354-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0354-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033956297","display_name":"Lucian Chan","orcid":"https://orcid.org/0000-0002-1223-0431"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lucian Chan","raw_affiliation_strings":["Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069354331","display_name":"Geoffrey Hutchison","orcid":"https://orcid.org/0000-0002-1757-1980"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Geoffrey R. Hutchison","raw_affiliation_strings":["Department of Chemistry and Chemical Engineering, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA. geoffh@pitt.edu","Department of Chemistry and Chemical Engineering, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Engineering, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA. geoffh@pitt.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Chemical Engineering, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011245839","display_name":"Garrett M. Morris","orcid":"https://orcid.org/0000-0003-1731-8405"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Garrett M. Morris","raw_affiliation_strings":["Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK","institution_ids":["https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5069354331"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.8451,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.91488731,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"11","issue":"1","first_page":"32","last_page":"32"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9991000294685364,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9991000294685364,"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":0.9983999729156494,"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/T12535","display_name":"Machine Learning and Data Classification","score":0.9544000029563904,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.9285394549369812},{"id":"https://openalex.org/keywords/maxima-and-minima","display_name":"Maxima and minima","score":0.8122198581695557},{"id":"https://openalex.org/keywords/random-search","display_name":"Random search","score":0.6687110662460327},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5680683255195618},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5522515773773193},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.41363653540611267},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.389054536819458},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3486081063747406},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.34776702523231506},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3063221573829651},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.2976663112640381},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23401665687561035},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19018131494522095},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.07872185111045837}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.9285394549369812},{"id":"https://openalex.org/C186633575","wikidata":"https://www.wikidata.org/wiki/Q845060","display_name":"Maxima and minima","level":2,"score":0.8122198581695557},{"id":"https://openalex.org/C126661757","wikidata":"https://www.wikidata.org/wiki/Q4925641","display_name":"Random search","level":2,"score":0.6687110662460327},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5680683255195618},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5522515773773193},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.41363653540611267},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.389054536819458},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3486081063747406},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.34776702523231506},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3063221573829651},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.2976663112640381},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23401665687561035},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19018131494522095},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.07872185111045837},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-019-0354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0354-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0354-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:31115707","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31115707","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:bdac2ad431034711afcb83fea6fe8d7d","is_oa":true,"landing_page_url":"https://doaj.org/article/bdac2ad431034711afcb83fea6fe8d7d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-11 (2019)","raw_type":"article"},{"id":"pmh:oai:ora.ox.ac.uk:uuid:afbf061e-f22b-4838-80fd-6e8ef04afd97","is_oa":true,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:afbf061e-f22b-4838-80fd-6e8ef04afd97","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6528340","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6528340","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"doi:10.6084/m9.figshare.c.4512884.v1","is_oa":true,"landing_page_url":"https://doi.org/10.6084/m9.figshare.c.4512884.v1","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-019-0354-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-019-0354-7","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-019-0354-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"awards":[{"id":"https://openalex.org/G1571791257","display_name":"EPSRC and MRC Centre for Doctoral Training in Systems Approaches to Biomedical Science","funder_award_id":"EP/L016044/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6446403202","display_name":null,"funder_award_id":"CHE-1800435","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G65555965","display_name":null,"funder_award_id":"EP/ L016044/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6763658222","display_name":"D3SC: CDS&E: Conformer Toolkit: Generating Accurate Small Molecule Conformer Ensembles","funder_award_id":"1800435","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8435008771","display_name":null,"funder_award_id":"CHE-1800435","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947658954.pdf","grobid_xml":"https://content.openalex.org/works/W2947658954.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W60686164","https://openalex.org/W824892955","https://openalex.org/W1583837637","https://openalex.org/W1746819321","https://openalex.org/W1976848779","https://openalex.org/W1983194490","https://openalex.org/W1999297737","https://openalex.org/W2001775135","https://openalex.org/W2015770960","https://openalex.org/W2032842297","https://openalex.org/W2052818547","https://openalex.org/W2053333781","https://openalex.org/W2072537419","https://openalex.org/W2078374001","https://openalex.org/W2099201756","https://openalex.org/W2100125011","https://openalex.org/W2114326383","https://openalex.org/W2127463492","https://openalex.org/W2130479394","https://openalex.org/W2131241448","https://openalex.org/W2140291772","https://openalex.org/W2146292423","https://openalex.org/W2147421370","https://openalex.org/W2152903006","https://openalex.org/W2169678694","https://openalex.org/W2192203593","https://openalex.org/W2220825152","https://openalex.org/W2240302289","https://openalex.org/W2244785476","https://openalex.org/W2437591545","https://openalex.org/W2461312660","https://openalex.org/W2587816047","https://openalex.org/W2622957538","https://openalex.org/W2726184500","https://openalex.org/W2761273232","https://openalex.org/W2761786744","https://openalex.org/W2789059526","https://openalex.org/W2888436131","https://openalex.org/W2913087274","https://openalex.org/W2950277768","https://openalex.org/W2951665052","https://openalex.org/W3098139325","https://openalex.org/W4211049957"],"related_works":["https://openalex.org/W2914914103","https://openalex.org/W1528449109","https://openalex.org/W4242940514","https://openalex.org/W2111639746","https://openalex.org/W241023412","https://openalex.org/W2995179471","https://openalex.org/W2056379908","https://openalex.org/W2803388586","https://openalex.org/W2803838371","https://openalex.org/W2003567321"],"abstract_inverted_index":{"Generating":[0],"low-energy":[1,122],"molecular":[2,14],"conformers":[3,29,137],"is":[4],"a":[5,43,61,166],"key":[6],"task":[7],"for":[8,54,170],"many":[9],"areas":[10],"of":[11,60,100,158],"computational":[12],"chemistry,":[13],"modeling":[15],"and":[16,71,90],"cheminformatics.":[17],"Most":[18],"current":[19],"conformer":[20,102],"generation":[21],"methods":[22],"primarily":[23],"focus":[24],"on":[25],"generating":[26],"geometrically":[27],"diverse":[28],"rather":[30],"than":[31,114,165],"finding":[32,55],"the":[33,49,56,83,98,101,159],"most":[34],"probable":[35],"or":[36,116,128,174],"energetically":[37],"lowest":[38,57,84],"minima.":[39,123],"Here,":[40],"we":[41,107],"present":[42],"new":[44],"stochastic":[45],"search":[46,73,103,119,169],"method":[47,81],"called":[48],"Bayesian":[50],"optimization":[51],"algorithm":[52],"(BOA)":[53],"energy":[58,146],"conformation":[59],"given":[62],"molecule.":[63],"We":[64],"compare":[65],"BOA":[66,109,142,161],"with":[67,126,172],"uniform":[68,117],"random":[69,118],"search,":[70,140],"systematic":[72,115,167],"as":[74],"implemented":[75],"in":[76,138],"Confab,":[77],"to":[78,96,120,148],"determine":[79],"which":[80],"finds":[82,162],"energy.":[85],"Energetic":[86],"difference,":[87],"root-mean-square":[88],"deviation,":[89],"torsion":[91],"fingerprint":[92],"deviation":[93],"are":[94],"used":[95],"quantify":[97],"performance":[99],"algorithms.":[104],"In":[105],"general,":[106],"find":[108,121,149],"requires":[110,144],"far":[111],"fewer":[112,155],"evaluations":[113,147],"For":[124],"molecules":[125,171],"four":[127,173],"more":[129,175],"rotatable":[130,176],"bonds,":[131],"Confab":[132,168],"typically":[133],"evaluates":[134],"$$10^{4}$$":[135],"(median)":[136],"its":[139],"while":[141],"only":[143],"$$10^{2}$$":[145],"top":[150],"candidates.":[151],"Despite":[152],"using":[153],"evaluating":[154],"conformers,":[156],"20\u201340%":[157],"time":[160],"lower-energy":[163],"conformations":[164],"bonds.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":8},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}