{"id":"https://openalex.org/W3181264219","doi":"https://doi.org/10.1093/bioinformatics/btab496","title":"ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution","display_name":"ClustENMD: efficient sampling of biomolecular conformational space at atomic resolution","publication_year":2021,"publication_date":"2021-07-03","ids":{"openalex":"https://openalex.org/W3181264219","doi":"https://doi.org/10.1093/bioinformatics/btab496","mag":"3181264219","pmid":"https://pubmed.ncbi.nlm.nih.gov/34240100"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab496","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab496","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3956/41091724/btab496.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3956/41091724/btab496.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030926045","display_name":"Burak Kaynak","orcid":"https://orcid.org/0000-0002-0897-2037"},"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":"Burak T Kaynak","raw_affiliation_strings":["Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042499227","display_name":"She Zhang","orcid":"https://orcid.org/0000-0001-9265-4498"},"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":"She Zhang","raw_affiliation_strings":["Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081814496","display_name":"\u0130vet Bahar","orcid":"https://orcid.org/0000-0001-9959-4176"},"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":false,"raw_author_name":"Ivet Bahar","raw_affiliation_strings":["Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080732397","display_name":"Pemra Doruker","orcid":"https://orcid.org/0000-0002-4824-2223"},"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":"Pemra Doruker","raw_affiliation_strings":["Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, PA 15260, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5030926045","https://openalex.org/A5042499227","https://openalex.org/A5080732397"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2173,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.7875359,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"37","issue":"21","first_page":"3956","last_page":"3958"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":1.0,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9997000098228455,"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":0.9943000078201294,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7258822917938232},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.6673600673675537},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.576935887336731},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4876200258731842},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4364062547683716},{"id":"https://openalex.org/keywords/subspace-topology","display_name":"Subspace topology","score":0.41186976432800293},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3983815312385559},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3795708417892456},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3690674304962158},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20939311385154724},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18433696031570435}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7258822917938232},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.6673600673675537},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.576935887336731},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4876200258731842},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4364062547683716},{"id":"https://openalex.org/C32834561","wikidata":"https://www.wikidata.org/wiki/Q660730","display_name":"Subspace topology","level":2,"score":0.41186976432800293},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3983815312385559},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3795708417892456},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3690674304962158},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20939311385154724},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18433696031570435},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","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/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab496","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab496","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3956/41091724/btab496.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34240100","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34240100","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:7463246","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8570821","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8570821","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8570821","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab496","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab496","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3956/41091724/btab496.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3104744183","display_name":null,"funder_award_id":"P41GM103712","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3181264219.pdf","grobid_xml":"https://content.openalex.org/works/W3181264219.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1970454429","https://openalex.org/W2039588355","https://openalex.org/W2059928115","https://openalex.org/W2113994268","https://openalex.org/W2123681603","https://openalex.org/W2124483575","https://openalex.org/W2130479394","https://openalex.org/W2140889378","https://openalex.org/W2142595184","https://openalex.org/W2161605421","https://openalex.org/W2164270482","https://openalex.org/W2322463084","https://openalex.org/W2404280981","https://openalex.org/W2469816127","https://openalex.org/W2491917380","https://openalex.org/W2609916011","https://openalex.org/W2916697533","https://openalex.org/W2949223833","https://openalex.org/W2969910143","https://openalex.org/W2973252091","https://openalex.org/W3036387766","https://openalex.org/W3039124487","https://openalex.org/W3088896002","https://openalex.org/W3129160401","https://openalex.org/W3140562424"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W2052399476","https://openalex.org/W2077273959","https://openalex.org/W2810163160","https://openalex.org/W2037964119","https://openalex.org/W1494829770","https://openalex.org/W4220905048","https://openalex.org/W4385077663"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}