{"id":"https://openalex.org/W2123681603","doi":"https://doi.org/10.1093/bioinformatics/btr168","title":"<i>ProDy</i>: Protein Dynamics Inferred from Theory and Experiments","display_name":"<i>ProDy</i>: Protein Dynamics Inferred from Theory and Experiments","publication_year":2011,"publication_date":"2011-04-05","ids":{"openalex":"https://openalex.org/W2123681603","doi":"https://doi.org/10.1093/bioinformatics/btr168","mag":"2123681603","pmid":"https://pubmed.ncbi.nlm.nih.gov/21471012"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr168","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1575/48863254/bioinformatics_27_11_1575.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/27/11/1575/48863254/bioinformatics_27_11_1575.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059756652","display_name":"Ahmet Bakan","orcid":"https://orcid.org/0000-0002-0399-0359"},"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":"Ahmet Bakan","raw_affiliation_strings":["Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046278102","display_name":"Lidio Meireles","orcid":null},"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":"Lidio M. Meireles","raw_affiliation_strings":["Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","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, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computational and Systems Biology, and Clinical & Translational Science Institute, School of Medicine, University of Pittsburgh, 3064 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213, USA","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059756652"],"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":12.4072,"has_fulltext":true,"cited_by_count":1170,"citation_normalized_percentile":{"value":0.99237655,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"27","issue":"11","first_page":"1575","last_page":"1577"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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":0.9962000250816345,"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/python","display_name":"Python (programming language)","score":0.824069082736969},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7573182582855225},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5808959007263184},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5698021650314331},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5134454965591431},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.4909570515155792},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36428073048591614},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3618077039718628},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3361310064792633},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2963714003562927}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.824069082736969},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7573182582855225},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5808959007263184},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5698021650314331},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5134454965591431},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.4909570515155792},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36428073048591614},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3618077039718628},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3361310064792633},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2963714003562927}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btr168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr168","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1575/48863254/bioinformatics_27_11_1575.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21471012","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21471012","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:CiteSeerX.psu:10.1.1.723.8546","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.723.8546","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.csb.pitt.edu/Faculty/bahar/publications/199.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:27/11/1575","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/11/1575","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3102222","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3102222","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr168","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr168","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/11/1575/48863254/bioinformatics_27_11_1575.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G2332707893","display_name":null,"funder_award_id":"RR024153","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7353379685","display_name":null,"funder_award_id":"UL1 RR024153","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/W2123681603.pdf","grobid_xml":"https://content.openalex.org/works/W2123681603.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W264357520","https://openalex.org/W1982211331","https://openalex.org/W1991764480","https://openalex.org/W2018748094","https://openalex.org/W2023857477","https://openalex.org/W2029667189","https://openalex.org/W2048910851","https://openalex.org/W2053893146","https://openalex.org/W2063962473","https://openalex.org/W2066926304","https://openalex.org/W2095509648","https://openalex.org/W2105254477","https://openalex.org/W2112033855","https://openalex.org/W2112315506","https://openalex.org/W2112712631","https://openalex.org/W2113971181","https://openalex.org/W2124483575","https://openalex.org/W2132589721","https://openalex.org/W2168172687","https://openalex.org/W2168211076","https://openalex.org/W2171537755","https://openalex.org/W6609861729"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4386463918","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4226320247","https://openalex.org/W4292228088"],"abstract_inverted_index":{"ProDy":[0],"is":[1],"open":[2],"source":[3],"and":[4],"freely":[5],"available":[6],"under":[7],"GNU":[8],"General":[9],"Public":[10],"License":[11],"from":[12],"http://www.csb.pitt.edu/ProDy/.":[13]},"counts_by_year":[{"year":2026,"cited_by_count":30},{"year":2025,"cited_by_count":129},{"year":2024,"cited_by_count":123},{"year":2023,"cited_by_count":93},{"year":2022,"cited_by_count":111},{"year":2021,"cited_by_count":124},{"year":2020,"cited_by_count":120},{"year":2019,"cited_by_count":87},{"year":2018,"cited_by_count":84},{"year":2017,"cited_by_count":69},{"year":2016,"cited_by_count":62},{"year":2015,"cited_by_count":45},{"year":2014,"cited_by_count":46},{"year":2013,"cited_by_count":18},{"year":2012,"cited_by_count":24}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2016-06-24T00:00:00"}
