{"id":"https://openalex.org/W2019691413","doi":"https://doi.org/10.1093/nar/gkn216","title":"The RosettaDock server for local protein-protein docking","display_name":"The RosettaDock server for local protein-protein docking","publication_year":2008,"publication_date":"2008-04-29","ids":{"openalex":"https://openalex.org/W2019691413","doi":"https://doi.org/10.1093/nar/gkn216","mag":"2019691413","pmid":"https://pubmed.ncbi.nlm.nih.gov/18442991"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn216","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W233/7624254/gkn216.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W233/7624254/gkn216.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075127527","display_name":"Sergey Lyskov","orcid":"https://orcid.org/0000-0001-6380-6712"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Lyskov","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering and Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering and Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA","institution_ids":["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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. J. Gray","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering and 2 Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering and 2 Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":8.2838,"has_fulltext":false,"cited_by_count":614,"citation_normalized_percentile":{"value":0.9828358,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"36","issue":"Web Server","first_page":"W233","last_page":"W238"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9975000023841858,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9926000237464905,"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/biology","display_name":"Biology","score":0.745257556438446},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.7103589773178101},{"id":"https://openalex.org/keywords/funnel","display_name":"Funnel","score":0.5394125580787659},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.48623958230018616},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4851111173629761},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.45985323190689087},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45317935943603516},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4147687554359436},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4116641879081726},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33653736114501953},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3028191924095154},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16922974586486816},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13595056533813477},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.13558301329612732},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11922484636306763}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.745257556438446},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.7103589773178101},{"id":"https://openalex.org/C17435862","wikidata":"https://www.wikidata.org/wiki/Q29957","display_name":"Funnel","level":2,"score":0.5394125580787659},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.48623958230018616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4851111173629761},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.45985323190689087},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45317935943603516},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4147687554359436},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4116641879081726},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33653736114501953},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3028191924095154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16922974586486816},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13595056533813477},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.13558301329612732},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11922484636306763},{"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/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"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":"D000465","descriptor_name":"Algorithms","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":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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D046912","descriptor_name":"Multiprotein Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkn216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn216","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W233/7624254/gkn216.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18442991","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18442991","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2447798","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447798","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn216","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W233/7624254/gkn216.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.800000011920929,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1607183863","https://openalex.org/W1968922152","https://openalex.org/W1989973265","https://openalex.org/W1992658340","https://openalex.org/W1999390565","https://openalex.org/W2009406517","https://openalex.org/W2018410079","https://openalex.org/W2025146643","https://openalex.org/W2028588417","https://openalex.org/W2030074569","https://openalex.org/W2047289990","https://openalex.org/W2066244933","https://openalex.org/W2071739012","https://openalex.org/W2076753628","https://openalex.org/W2096259534","https://openalex.org/W2104948862","https://openalex.org/W2106222602","https://openalex.org/W2111387452","https://openalex.org/W2112743424","https://openalex.org/W2113885150","https://openalex.org/W2115167726","https://openalex.org/W2122084284","https://openalex.org/W2123028643","https://openalex.org/W2130031978","https://openalex.org/W2130479394","https://openalex.org/W2133712572","https://openalex.org/W2134059200","https://openalex.org/W2137167381","https://openalex.org/W2138579861","https://openalex.org/W2145793759","https://openalex.org/W2151460035","https://openalex.org/W2151667626","https://openalex.org/W2153255725","https://openalex.org/W2160223767","https://openalex.org/W2164130591","https://openalex.org/W2166317516","https://openalex.org/W2167581550"],"related_works":["https://openalex.org/W2131900949","https://openalex.org/W3158075195","https://openalex.org/W3138089182","https://openalex.org/W3187431608","https://openalex.org/W1974422922","https://openalex.org/W4309353019","https://openalex.org/W2914490533","https://openalex.org/W2097217326","https://openalex.org/W2145118195","https://openalex.org/W3118344282"],"abstract_inverted_index":{"The":[0,23],"RosettaDock":[1,38,82],"server":[2,24,45],"(http://rosettadock.graylab.jhu.edu)":[3],"identifies":[4],"low-energy":[5],"conformations":[6],"of":[7,61,65,67,77,96],"a":[8,12,32],"protein-protein":[9],"interaction":[10],"near":[11],"given":[13],"starting":[14,33],"configuration":[15],"by":[16],"optimizing":[17],"rigid-body":[18],"orientation":[19],"and":[20,31,43,50,91],"side-chain":[21],"conformations.":[22],"requires":[25],"two":[26],"protein":[27],"structures":[28],"as":[29],"inputs":[30],"location":[34],"for":[35,54],"the":[36,44,55,62,68,73,87,93],"search.":[37],"generates":[39],"1000":[40,69],"independent":[41],"structures,":[42],"returns":[46],"pictures,":[47],"coordinate":[48],"files":[49],"detailed":[51],"scoring":[52],"information":[53],"10":[56],"top-scoring":[57],"models.":[58],"A":[59],"plot":[60],"total":[63],"energy":[64],"each":[66],"models":[70],"created":[71],"shows":[72],"presence":[74],"or":[75],"absence":[76],"an":[78],"energetic":[79],"binding":[80],"funnel.":[81],"has":[83],"been":[84],"validated":[85],"on":[86],"docking":[88],"benchmark":[89],"set":[90],"through":[92],"Critical":[94],"Assessment":[95],"PRedicted":[97],"Interactions":[98],"blind":[99],"prediction":[100],"challenge.":[101]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":39},{"year":2024,"cited_by_count":47},{"year":2023,"cited_by_count":36},{"year":2022,"cited_by_count":49},{"year":2021,"cited_by_count":54},{"year":2020,"cited_by_count":42},{"year":2019,"cited_by_count":35},{"year":2018,"cited_by_count":31},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":44},{"year":2015,"cited_by_count":32},{"year":2014,"cited_by_count":33},{"year":2013,"cited_by_count":42},{"year":2012,"cited_by_count":31}],"updated_date":"2026-06-16T09:24:06.705377","created_date":"2025-10-10T00:00:00"}
