{"id":"https://openalex.org/W2116345848","doi":"https://doi.org/10.1186/1758-2946-3-9","title":"PubChem3D: Diversity of shape","display_name":"PubChem3D: Diversity of shape","publication_year":2011,"publication_date":"2011-03-21","ids":{"openalex":"https://openalex.org/W2116345848","doi":"https://doi.org/10.1186/1758-2946-3-9","mag":"2116345848","pmid":"https://pubmed.ncbi.nlm.nih.gov/21418625"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-9","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-9","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/10.1186/1758-2946-3-9","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"]}],"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. 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"],"raw_orcid":null,"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":["https://openalex.org/I4210109390"]},{"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"]}]},{"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/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":"Sunghwan Kim","raw_affiliation_strings":["Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040349721","display_name":"Stephen H. Bryant","orcid":null},"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":"Stephen H Bryant","raw_affiliation_strings":["Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":2.9751,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.91442831,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.2637999951839447,"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":0.2637999951839447,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.1850000023841858,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12613","display_name":"X-ray Diffraction in Crystallography","score":0.08030000329017639,"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/computer-science","display_name":"Computer science","score":0.6328065991401672},{"id":"https://openalex.org/keywords/diversity","display_name":"Diversity (politics)","score":0.624237596988678},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4928036034107208},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35462862253189087},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34882450103759766},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.06745168566703796}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6328065991401672},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.624237596988678},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4928036034107208},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35462862253189087},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34882450103759766},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.06745168566703796},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-3-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-9","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-9","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:21418625","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21418625","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:5885cf9aba834255bfd557c5ca05e41f","is_oa":true,"landing_page_url":"https://doaj.org/article/5885cf9aba834255bfd557c5ca05e41f","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 3, Iss 1, p 9 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2083872","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3072936","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:10.1186/1758-2946-3-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-9","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-9","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":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"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/W2116345848.pdf","grobid_xml":"https://content.openalex.org/works/W2116345848.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1578560356","https://openalex.org/W1601495365","https://openalex.org/W1998848097","https://openalex.org/W2009000921","https://openalex.org/W2027065525","https://openalex.org/W2038361288","https://openalex.org/W2039197391","https://openalex.org/W2060153789","https://openalex.org/W2080886752","https://openalex.org/W2087179087","https://openalex.org/W2096525273","https://openalex.org/W2103311408","https://openalex.org/W2125792789","https://openalex.org/W2127553917","https://openalex.org/W2144659448","https://openalex.org/W2160205549","https://openalex.org/W2163240555","https://openalex.org/W2170481351","https://openalex.org/W2260675179","https://openalex.org/W2488677743","https://openalex.org/W4210483668","https://openalex.org/W4230466483","https://openalex.org/W4231041617"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,30,58,115,162],"shape":[2,33,40,63,70,105,109,123,145,166,174,208],"diversity":[3,31,146,167,206],"of":[4,26,32,50,55,60,82,92,111,117,125,143,147,153,165,171,182,207],"16.4":[5],"million":[6],"biologically":[7],"relevant":[8],"molecules":[9],"from":[10,194],"the":[11,39,48,90,108,122,144,151,154,180,192,204],"PubChem":[12,185],"Compound":[13],"database":[14],"and":[15,97,173],"their":[16,98],"1.46":[17],"billion":[18],"diverse":[19],"conformers":[20,93],"was":[21,35,73,85,128,132,138],"explored":[22],"as":[23,65,79,168],"a":[24,45,68,80,102,118,135,169,200],"function":[25,81,170],"molecular":[27],"volume.":[28,57,83],"RESULTS:":[29],"space":[34,110,124],"investigated":[36],"by":[37,67],"determining":[38],"similarity":[41,71,175],"threshold":[42],"to":[43,75,120,140,203],"achieve":[44],"maximum":[46],"on":[47],"count":[49,91],"reference":[51,104],"shapes":[52],"per":[53,94],"unit":[54,95],"conformer":[56],"rate":[59],"growth":[61,164],"in":[62,158,184],"space,":[64],"represented":[66],"decreasing":[69],"threshold,":[72],"found":[74],"be":[76,198],"remarkably":[77],"smooth":[78],"There":[84],"no":[86],"apparent":[87],"correlation":[88],"between":[89],"volume":[96,119,137,155,172],"diversity,":[99],"meaning":[100],"that":[101,134],"single":[103],"can":[106],"describe":[107,121,141],"many":[112],"chemical":[113],"structures.":[114],"ability":[116],"lesser":[126,148],"volumes":[127],"also":[129],"examined.":[130],"It":[131],"shown":[133],"given":[136],"able":[139],"40-70%":[142],"volumes,":[149],"for":[150],"majority":[152],"range":[156],"considered":[157,199],"this":[159,195],"study.":[160],"CONCLUSION:":[161],"relative":[163],"is":[176,188],"surprisingly":[177],"uniform.":[178],"Given":[179],"distribution":[181],"chemicals":[183],"versus":[186],"what":[187],"theoretically":[189],"synthetically":[190],"possible,":[191],"results":[193],"analysis":[196],"should":[197],"conservative":[201],"estimate":[202],"true":[205],"space.":[209]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
