{"id":"https://openalex.org/W2153057704","doi":"https://doi.org/10.1186/1758-2946-3-26","title":"PubChem3D: Biologically relevant 3-D similarity","display_name":"PubChem3D: Biologically relevant 3-D similarity","publication_year":2011,"publication_date":"2011-07-22","ids":{"openalex":"https://openalex.org/W2153057704","doi":"https://doi.org/10.1186/1758-2946-3-26","mag":"2153057704","pmid":"https://pubmed.ncbi.nlm.nih.gov/21781288"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-26","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/10.1186/1758-2946-3-26","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"]},{"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":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, 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/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":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"],"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/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":["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/A5100430147"],"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":2.6044,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.9001621,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"3","issue":"1","first_page":"26","last_page":"26"},"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":0.9980999827384949,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9958999752998352,"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/pubchem","display_name":"PubChem","score":0.9858115315437317},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7835047245025635},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.6998867988586426},{"id":"https://openalex.org/keywords/chemical-similarity","display_name":"Chemical similarity","score":0.49286866188049316},{"id":"https://openalex.org/keywords/biological-activity","display_name":"Biological activity","score":0.4483189582824707},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.44079506397247314},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.4256443977355957},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4205663800239563},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41967886686325073},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32670891284942627},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32560306787490845},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.30903899669647217},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2944772243499756},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.28275230526924133},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22102096676826477},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.17146334052085876},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14650869369506836},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.12264075875282288}],"concepts":[{"id":"https://openalex.org/C158180186","wikidata":"https://www.wikidata.org/wiki/Q278487","display_name":"PubChem","level":2,"score":0.9858115315437317},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7835047245025635},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.6998867988586426},{"id":"https://openalex.org/C24259465","wikidata":"https://www.wikidata.org/wiki/Q2272153","display_name":"Chemical similarity","level":3,"score":0.49286866188049316},{"id":"https://openalex.org/C116073593","wikidata":"https://www.wikidata.org/wiki/Q864491","display_name":"Biological activity","level":3,"score":0.4483189582824707},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.44079506397247314},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.4256443977355957},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4205663800239563},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41967886686325073},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32670891284942627},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32560306787490845},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30903899669647217},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2944772243499756},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.28275230526924133},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22102096676826477},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.17146334052085876},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14650869369506836},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.12264075875282288},{"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},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"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/C202751555","wikidata":"https://www.wikidata.org/wiki/Q221681","display_name":"In vitro","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1758-2946-3-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-26","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:21781288","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21781288","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:0e587b3f1e804fd9a416df9bd338ddd1","is_oa":true,"landing_page_url":"https://doaj.org/article/0e587b3f1e804fd9a416df9bd338ddd1","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 26 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2223468","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3223603","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:10.1186/1758-2946-3-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-26","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-26","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/W2153057704.pdf","grobid_xml":"https://content.openalex.org/works/W2153057704.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W41967644","https://openalex.org/W1601495365","https://openalex.org/W1605923270","https://openalex.org/W1968410036","https://openalex.org/W1970062872","https://openalex.org/W1970651561","https://openalex.org/W1985036373","https://openalex.org/W1998263233","https://openalex.org/W2011570269","https://openalex.org/W2013068027","https://openalex.org/W2022478977","https://openalex.org/W2031591152","https://openalex.org/W2036978594","https://openalex.org/W2038609448","https://openalex.org/W2039609876","https://openalex.org/W2060153789","https://openalex.org/W2060415844","https://openalex.org/W2065915163","https://openalex.org/W2067490054","https://openalex.org/W2075186867","https://openalex.org/W2080886752","https://openalex.org/W2085379340","https://openalex.org/W2096525273","https://openalex.org/W2097449851","https://openalex.org/W2097654801","https://openalex.org/W2116345848","https://openalex.org/W2116855266","https://openalex.org/W2125792789","https://openalex.org/W2127553917","https://openalex.org/W2135812506","https://openalex.org/W2139731838","https://openalex.org/W2144659448","https://openalex.org/W2156077095","https://openalex.org/W2158721366","https://openalex.org/W2170481351","https://openalex.org/W2949291136","https://openalex.org/W2949611276","https://openalex.org/W4231041617"],"related_works":["https://openalex.org/W2146844279","https://openalex.org/W2153057704","https://openalex.org/W2940362127","https://openalex.org/W2113373093","https://openalex.org/W2114704115","https://openalex.org/W2078530460","https://openalex.org/W3022702824","https://openalex.org/W4388961610","https://openalex.org/W2959376435","https://openalex.org/W2121202200"],"abstract_inverted_index":{"This":[0],"study":[1],"provides":[2],"a":[3,23,28],"statistical":[4],"guideline":[5],"for":[6],"analyzing":[7],"biological":[8],"assay":[9],"data":[10],"in":[11],"terms":[12],"of":[13,32],"3-D":[14],"similarity":[15],"and":[16],"PubChem":[17],"structure-activity":[18],"analysis":[19],"tools.":[20],"When":[21],"using":[22],"single":[24],"conformer":[25],"per":[26],"compound,":[27],"relatively":[29],"small":[30],"number":[31],"assays":[33],"appear":[34],"to":[35,38],"be":[36],"able":[37],"separate":[39],"\"active/active\"":[40],"space":[41],"from":[42],"\"active/inactive\"":[43],"space.":[44]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
