{"id":"https://openalex.org/W2170481351","doi":"https://doi.org/10.1186/1758-2946-3-4","title":"PubChem3D: Conformer generation","display_name":"PubChem3D: Conformer generation","publication_year":2011,"publication_date":"2011-01-27","ids":{"openalex":"https://openalex.org/W2170481351","doi":"https://doi.org/10.1186/1758-2946-3-4","mag":"2170481351","pmid":"https://pubmed.ncbi.nlm.nih.gov/21272340"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-4","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/10.1186/1758-2946-3-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015494748","display_name":"Evan Bolton","orcid":"https://orcid.org/0000-0002-5959-6190"},"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":true,"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. bolton@ncbi.nlm.nih.gov","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"],"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, 8600 Rockville Pike, Bethesda, MD, 20894, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100430147","display_name":"Sunghwan Kim","orcid":"https://orcid.org/0000-0001-9828-2074"},"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":"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"],"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"]}]},{"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"],"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"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015494748"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":3.2546,"has_fulltext":true,"cited_by_count":42,"citation_normalized_percentile":{"value":0.92345679,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"3","issue":"1","first_page":"4","last_page":"4"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9891999959945679,"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":0.9768999814987183,"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":0.9787197113037109},{"id":"https://openalex.org/keywords/pubchem","display_name":"PubChem","score":0.7473435997962952},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5290138721466064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5104250311851501},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.4773321747779846},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4758869409561157},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4634447395801544},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.44367504119873047},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.42562413215637207},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40720680356025696},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.36482489109039307},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3480251431465149},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2508534789085388},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08491787314414978}],"concepts":[{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.9787197113037109},{"id":"https://openalex.org/C158180186","wikidata":"https://www.wikidata.org/wiki/Q278487","display_name":"PubChem","level":2,"score":0.7473435997962952},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5290138721466064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5104250311851501},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4773321747779846},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4758869409561157},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4634447395801544},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.44367504119873047},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.42562413215637207},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40720680356025696},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.36482489109039307},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3480251431465149},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2508534789085388},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08491787314414978},{"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/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},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-4","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:21272340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21272340","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:c1f8aa89316e487cb1c01cf317bd1bed","is_oa":true,"landing_page_url":"https://doaj.org/article/c1f8aa89316e487cb1c01cf317bd1bed","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":"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 3, Iss 1, p 4 (2011)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3042967","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3042967","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-4","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-4","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","score":0.8799999952316284,"id":"https://metadata.un.org/sdg/7"}],"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/W2170481351.pdf","grobid_xml":"https://content.openalex.org/works/W2170481351.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W966084261","https://openalex.org/W1497828738","https://openalex.org/W1531550633","https://openalex.org/W1578560356","https://openalex.org/W1601495365","https://openalex.org/W1971572370","https://openalex.org/W1973056533","https://openalex.org/W1986139296","https://openalex.org/W2002755329","https://openalex.org/W2003861094","https://openalex.org/W2037111659","https://openalex.org/W2044038786","https://openalex.org/W2057491831","https://openalex.org/W2058107752","https://openalex.org/W2061098698","https://openalex.org/W2071579644","https://openalex.org/W2075186867","https://openalex.org/W2078374001","https://openalex.org/W2080886752","https://openalex.org/W2094839792","https://openalex.org/W2096525273","https://openalex.org/W2102017976","https://openalex.org/W2121853844","https://openalex.org/W2127553917","https://openalex.org/W2130479394","https://openalex.org/W2138473864","https://openalex.org/W2144571979","https://openalex.org/W2144659448","https://openalex.org/W2147421370","https://openalex.org/W2156207120","https://openalex.org/W2166114438","https://openalex.org/W2210622668","https://openalex.org/W2949387234","https://openalex.org/W4210483668","https://openalex.org/W4230224839","https://openalex.org/W4231041617","https://openalex.org/W6812332919"],"related_works":["https://openalex.org/W2104366126","https://openalex.org/W2547231910","https://openalex.org/W2235675062","https://openalex.org/W2148970764","https://openalex.org/W2011402683","https://openalex.org/W2146844279","https://openalex.org/W2079298303","https://openalex.org/W2014586343","https://openalex.org/W2111131931","https://openalex.org/W2010826470"],"abstract_inverted_index":{"Optimal":[0],"parameters":[1,38],"for":[2],"conformer":[3,36,53],"generation":[4,37],"using":[5],"OMEGA":[6],"were":[7],"explored":[8],"and":[9,39],"determined.":[10],"An":[11],"equation":[12],"was":[13],"developed":[14],"that":[15,23],"provides":[16],"an":[17],"RMSD":[18,40],"sampling":[19,41],"value":[20],"to":[21,30,50],"use":[22],"is":[24],"based":[25],"on":[26],"the":[27,47],"relative":[28],"accuracy":[29],"reproduce":[31],"bioactive":[32],"conformations.":[33],"The":[34],"optimal":[35],"values":[42],"determined":[43],"are":[44],"used":[45],"by":[46],"PubChem3D":[48],"project":[49],"generate":[51],"theoretical":[52],"models.":[54]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-18T14:38:29.013473","created_date":"2025-10-10T00:00:00"}
