{"id":"https://openalex.org/W2146844279","doi":"https://doi.org/10.1186/1758-2946-5-1","title":"PubChem3D: conformer ensemble accuracy","display_name":"PubChem3D: conformer ensemble accuracy","publication_year":2013,"publication_date":"2013-01-07","ids":{"openalex":"https://openalex.org/W2146844279","doi":"https://doi.org/10.1186/1758-2946-5-1","mag":"2146844279","pmid":"https://pubmed.ncbi.nlm.nih.gov/23289532"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-5-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-1","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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100430147","display_name":"Sunghwan Kim","orcid":"https://orcid.org/0000-0001-9828-2074"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sunghwan Kim","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov","National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov","institution_ids":[]},{"raw_affiliation_string":"National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015494748","display_name":"Evan Bolton","orcid":"https://orcid.org/0000-0002-5959-6190"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Evan E Bolton","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD, 20894, USA","National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040349721","display_name":"Stephen H. Bryant","orcid":null},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephen H Bryant","raw_affiliation_strings":["National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD, 20894, USA","National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Center for Biotechnology Information National Library of Medicine, National Institutes of Health Department of Health and Human Services, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100430147"],"corresponding_institution_ids":["https://openalex.org/I1299303238"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":7.7672,"has_fulltext":true,"cited_by_count":98,"citation_normalized_percentile":{"value":0.97823405,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"5","issue":"1","first_page":"1","last_page":"1"},"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9945999979972839,"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/T10640","display_name":"Spectroscopy and Chemometric Analyses","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.9913197755813599},{"id":"https://openalex.org/keywords/pubchem","display_name":"PubChem","score":0.9469796419143677},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5569583177566528},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5497270226478577},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4887528419494629},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.4429197907447815},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4187763035297394},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3990098237991333},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.37779149413108826},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3441142737865448},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3433883786201477},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2827165126800537},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.09851926565170288}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.9913197755813599},{"id":"https://openalex.org/C158180186","wikidata":"https://www.wikidata.org/wiki/Q278487","display_name":"PubChem","level":2,"score":0.9469796419143677},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5569583177566528},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5497270226478577},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4887528419494629},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4429197907447815},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4187763035297394},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3990098237991333},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.37779149413108826},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3441142737865448},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3433883786201477},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2827165126800537},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.09851926565170288},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-5-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-1","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:23289532","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23289532","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:b5111ecaea8241259801756773061488","is_oa":true,"landing_page_url":"https://doaj.org/article/b5111ecaea8241259801756773061488","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 5, Iss 1, p 1 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2551804","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3547714","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-5-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-5-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-5-1","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2146844279.pdf","grobid_xml":"https://content.openalex.org/works/W2146844279.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W966084261","https://openalex.org/W1497828738","https://openalex.org/W1531550633","https://openalex.org/W1601495365","https://openalex.org/W1973056533","https://openalex.org/W1986139296","https://openalex.org/W2002755329","https://openalex.org/W2003861094","https://openalex.org/W2008732224","https://openalex.org/W2013068027","https://openalex.org/W2013083986","https://openalex.org/W2019538911","https://openalex.org/W2020429677","https://openalex.org/W2037111659","https://openalex.org/W2038840577","https://openalex.org/W2044038786","https://openalex.org/W2058107752","https://openalex.org/W2061098698","https://openalex.org/W2071579644","https://openalex.org/W2075186867","https://openalex.org/W2076942392","https://openalex.org/W2078374001","https://openalex.org/W2080886752","https://openalex.org/W2090431249","https://openalex.org/W2094493457","https://openalex.org/W2094839792","https://openalex.org/W2096525273","https://openalex.org/W2102017976","https://openalex.org/W2112990058","https://openalex.org/W2116345848","https://openalex.org/W2117254509","https://openalex.org/W2127553917","https://openalex.org/W2130479394","https://openalex.org/W2131639373","https://openalex.org/W2135812506","https://openalex.org/W2138473864","https://openalex.org/W2144643488","https://openalex.org/W2144659448","https://openalex.org/W2147421370","https://openalex.org/W2153057704","https://openalex.org/W2156207120","https://openalex.org/W2164045406","https://openalex.org/W2168941972","https://openalex.org/W2169546341","https://openalex.org/W2170481351","https://openalex.org/W4230224839","https://openalex.org/W4244606935"],"related_works":["https://openalex.org/W2104366126","https://openalex.org/W2547231910","https://openalex.org/W2235675062","https://openalex.org/W2177317049","https://openalex.org/W4293208996","https://openalex.org/W2169546341","https://openalex.org/W2127553917","https://openalex.org/W2013068027","https://openalex.org/W2146844279","https://openalex.org/W2010826470"],"abstract_inverted_index":{"This":[0,78],"study":[1],"shows":[2,27],"the":[3,8,18,50,59,84],"RMSD":[4],"accuracy":[5,36,53,80],"performance":[6],"of":[7,20,34,54,58,71],"PubChem3D":[9,21,60],"conformer":[10],"models":[11],"is":[12,30],"operating":[13],"as":[14,83],"designed.":[15],"In":[16],"addition,":[17],"effect":[19],"sampling":[22],"on":[23],"3-D":[24],"similarity":[25],"measures":[26],"that":[28],"there":[29],"a":[31],"linear":[32],"degradation":[33],"average":[35],"with":[37],"respect":[38],"to":[39,62],"molecular":[40],"size":[41],"and":[42,67,75],"flexibility.":[43],"Generally":[44],"speaking,":[45],"one":[46],"can":[47],"likely":[48],"expect":[49],"worst-case":[51],"minimum":[52],"90%":[55],"or":[56,88],"more":[57],"ensembles":[61],"be":[63],"0.75,":[64],"1.09,":[65],"0.43,":[66],"1.13,":[68],"in":[69],"terms":[70],"STST-opt,":[72],"ComboTST-opt,":[73],"CTCT-opt,":[74],"ComboTCT-opt,":[76],"respectively.":[77],"expected":[79],"improves":[81],"linearly":[82],"molecule":[85],"becomes":[86],"smaller":[87],"less":[89],"flexible.":[90]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":9},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}