{"id":"https://openalex.org/W2151581834","doi":"https://doi.org/10.1093/bioinformatics/btq007","title":"PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta","display_name":"PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta","publication_year":2010,"publication_date":"2010-01-07","ids":{"openalex":"https://openalex.org/W2151581834","doi":"https://doi.org/10.1093/bioinformatics/btq007","mag":"2151581834","pmid":"https://pubmed.ncbi.nlm.nih.gov/20061306"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/5/689/48860623/bioinformatics_26_5_689.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/5/689/48860623/bioinformatics_26_5_689.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089946703","display_name":"Sidhartha Chaudhury","orcid":"https://orcid.org/0000-0001-9513-6688"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sidhartha Chaudhury","raw_affiliation_strings":["1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075127527","display_name":"Sergey Lyskov","orcid":"https://orcid.org/0000-0001-6380-6712"},"institutions":[{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sergey Lyskov","raw_affiliation_strings":["1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009383312","display_name":"Jeffrey J. Gray","orcid":"https://orcid.org/0000-0001-6380-2324"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I4210164401","display_name":"Sidney Kimmel Comprehensive Cancer Center","ror":"https://ror.org/05m5b8x20","country_code":"US","type":"facility","lineage":["https://openalex.org/I2799853436","https://openalex.org/I4210164401"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jeffrey J. Gray","raw_affiliation_strings":["1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Molecular Biophysics, 2 Department of Chemical and Biomolecular Engineering and 3 Institute of NanoBioTechnology, Sidney Kimmel Comprehensive Cancer Center and Institute of Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I4210164401","https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009383312"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I4210164401"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.9638,"has_fulltext":false,"cited_by_count":883,"citation_normalized_percentile":{"value":0.97136564,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"26","issue":"5","first_page":"689","last_page":"691"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9991000294685364,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9944999814033508,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.9351068735122681},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8257920742034912},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.8108625411987305},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5197858214378357},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4912371039390564},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.48571261763572693},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.41351091861724854},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34713026881217957},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.2892128825187683}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.9351068735122681},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8257920742034912},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.8108625411987305},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5197858214378357},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4912371039390564},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.48571261763572693},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.41351091861724854},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34713026881217957},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2892128825187683},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":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":"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},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btq007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/5/689/48860623/bioinformatics_26_5_689.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20061306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20061306","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:2049215","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2828115","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq007","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/5/689/48860623/bioinformatics_26_5_689.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310145","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95"},{"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/W2151581834.pdf","grobid_xml":"https://content.openalex.org/works/W2151581834.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W85593233","https://openalex.org/W255996521","https://openalex.org/W1968713350","https://openalex.org/W1969644422","https://openalex.org/W2004461664","https://openalex.org/W2007804411","https://openalex.org/W2015392953","https://openalex.org/W2019691413","https://openalex.org/W2071200955","https://openalex.org/W2071739012","https://openalex.org/W2103591844","https://openalex.org/W2114850508","https://openalex.org/W2115167726","https://openalex.org/W2117020466","https://openalex.org/W2135815512","https://openalex.org/W2145653677","https://openalex.org/W2150192011"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919","https://openalex.org/W3084909426"],"abstract_inverted_index":{"PyRosetta":[0],"is":[1,13],"a":[2],"stand-alone":[3],"package":[4],"available":[5,31],"at":[6],"http://www.pyrosetta.org":[7],"under":[8],"the":[9,33],"Rosetta":[10],"license":[11],"which":[12],"free":[14],"for":[15],"academic":[16],"and":[17,24],"non-profit":[18],"users.":[19],"A":[20],"tutorial,":[21],"user's":[22],"manual":[23],"sample":[25],"scripts":[26],"demonstrating":[27],"usage":[28],"are":[29],"also":[30],"on":[32],"web":[34],"site.":[35]},"counts_by_year":[{"year":2026,"cited_by_count":30},{"year":2025,"cited_by_count":121},{"year":2024,"cited_by_count":114},{"year":2023,"cited_by_count":103},{"year":2022,"cited_by_count":108},{"year":2021,"cited_by_count":109},{"year":2020,"cited_by_count":80},{"year":2019,"cited_by_count":40},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":33},{"year":2016,"cited_by_count":36},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":18},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":11}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
