{"id":"https://openalex.org/W2063597362","doi":"https://doi.org/10.1002/prot.20733","title":"Prediction of CASP6 structures using automated robetta protocols","display_name":"Prediction of CASP6 structures using automated robetta protocols","publication_year":2005,"publication_date":"2005-01-01","ids":{"openalex":"https://openalex.org/W2063597362","doi":"https://doi.org/10.1002/prot.20733","mag":"2063597362","pmid":"https://pubmed.ncbi.nlm.nih.gov/16187358"},"language":"en","primary_location":{"id":"doi:10.1002/prot.20733","doi":"https://doi.org/10.1002/prot.20733","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.20733","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029432420","display_name":"Dylan C. Chivian","orcid":"https://orcid.org/0000-0001-8189-8729","observed_orcids":["https://orcid.org/0000-0001-8189-8729"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dylan Chivian","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington","Dylan Chivian and David E. Kim contributed equally to this paper"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Dylan Chivian and David E. Kim contributed equally to this paper","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058714580","display_name":"David E. Kim","orcid":"https://orcid.org/0000-0002-0023-956X","observed_orcids":["https://orcid.org/0000-0002-0023-956X"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David E. Kim","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington","Dylan Chivian and David E. Kim contributed equally to this paper"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Dylan Chivian and David E. Kim contributed equally to this paper","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089221737","display_name":"Lars Malmstr\u00f6m","orcid":"https://orcid.org/0000-0001-9885-9312","observed_orcids":["https://orcid.org/0000-0001-9885-9312"]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lars Malmstr\u00f6m","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054083825","display_name":"Jack Schonbrun","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack Schonbrun","raw_affiliation_strings":["Howard Hughes Medical Institute, Seattle, Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, Seattle, Washington","institution_ids":["https://openalex.org/I1344073410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040573334","display_name":"Carol A. Rohl","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carol A. Rohl","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California, Santa Cruz, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California, Santa Cruz, California","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053192926","display_name":"David A. Baker","orcid":"https://orcid.org/0000-0001-7896-6217","observed_orcids":["https://orcid.org/0000-0001-7896-6217"]},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Baker","raw_affiliation_strings":["Department of Biochemistry, University of Washington, Seattle, Washington","Howard Hughes Medical Institute, Seattle, Washington"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Washington, Seattle, Washington","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, Seattle, Washington","institution_ids":["https://openalex.org/I1344073410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5053192926"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I201448701"],"apc_list":{"value":4550,"currency":"USD","value_usd":4550},"apc_paid":null,"fwci":7.0273,"has_fulltext":false,"cited_by_count":147,"citation_normalized_percentile":{"value":0.98154357,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"61","issue":"S7","first_page":"157","last_page":"166"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9940999746322632,"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":0.9940999746322632,"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":0.003800000064074993,"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":0.0003000000142492354,"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/protein-structure-prediction","display_name":"protein structure prediction","score":0.7929999828338623},{"id":"https://openalex.org/keywords/caspase-6","display_name":"caspase-6","score":0.7760000228881836},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"homology modeling","score":0.7739999890327454},{"id":"https://openalex.org/keywords/de-novo-structure-prediction","display_name":"de novo structure prediction","score":0.8740000128746033},{"id":"https://openalex.org/keywords/rosetta-spacecraft","display_name":"Rosetta","score":0.9419999718666077}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6967445611953735},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.5970754623413086},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07151985168457031},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D009010","descriptor_name":"Monte Carlo Method","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":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1002/prot.20733","doi":"https://doi.org/10.1002/prot.20733","is_oa":false,"landing_page_url":"https://doi.org/10.1002/prot.20733","pdf_url":null,"source":{"id":"https://openalex.org/S121161810","display_name":"Proteins Structure Function and Bioinformatics","issn_l":"0887-3585","issn":["0887-3585","1097-0134"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2"],"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proteins: Structure, Function, and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16187358","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16187358","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,"listed_in":[],"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":"Proteins","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W42096393","https://openalex.org/W1548178570","https://openalex.org/W1965206855","https://openalex.org/W1971596502","https://openalex.org/W1991962290","https://openalex.org/W2003852785","https://openalex.org/W2004228538","https://openalex.org/W2032443627","https://openalex.org/W2051019453","https://openalex.org/W2055118532","https://openalex.org/W2061033843","https://openalex.org/W2063581254","https://openalex.org/W2067484689","https://openalex.org/W2072645500","https://openalex.org/W2084466582","https://openalex.org/W2085277871","https://openalex.org/W2091194233","https://openalex.org/W2098487344","https://openalex.org/W2102533986","https://openalex.org/W2107538253","https://openalex.org/W2108376320","https://openalex.org/W2110483430","https://openalex.org/W2110922456","https://openalex.org/W2112615307","https://openalex.org/W2113403117","https://openalex.org/W2115167726","https://openalex.org/W2126016150","https://openalex.org/W2130479394","https://openalex.org/W2133312664","https://openalex.org/W2135815512","https://openalex.org/W2140244239","https://openalex.org/W2141216359","https://openalex.org/W2141783940","https://openalex.org/W2141885858","https://openalex.org/W2143210482","https://openalex.org/W2144483796","https://openalex.org/W2145149019","https://openalex.org/W2147059525","https://openalex.org/W2147667050","https://openalex.org/W2153187042","https://openalex.org/W2154106236","https://openalex.org/W2156469184","https://openalex.org/W2158307923","https://openalex.org/W2158714788","https://openalex.org/W2164130591","https://openalex.org/W2170962128","https://openalex.org/W4253986630","https://openalex.org/W6680848828"],"related_works":["https://openalex.org/W7098452719","https://openalex.org/W2145149019","https://openalex.org/W7100069607","https://openalex.org/W7099237485","https://openalex.org/W2017699309","https://openalex.org/W2115167726","https://openalex.org/W4253986630","https://openalex.org/W2157206486","https://openalex.org/W2091194233","https://openalex.org/W7096515290"],"abstract_inverted_index":{"The":[0,88],"Robetta":[1,15,77],"server":[2,23,50,78],"and":[3,31],"revised":[4],"automatic":[5],"protocols":[6,96],"were":[7,62],"used":[8],"to":[9,52,64],"predict":[10],"structures":[11],"for":[12,83],"CASP6":[13],"targets.":[14,87],"is":[16,108],"a":[17],"publicly":[18],"available":[19],"protein":[20],"structure":[21,34],"prediction":[22,35],"(http://robetta.bakerlab.org/":[24],"that":[25,61,75,94],"uses":[26],"the":[27,41,45,49,71,76,80,84,104],"Rosetta":[28],"de":[29],"novo":[30],"homology":[32],"modeling":[33],"methods.":[36],"We":[37,56,73],"incorporated":[38],"some":[39],"of":[40],"lessons":[42],"learned":[43],"in":[44,54,101,111],"CASP5":[46],"experiment":[47],"into":[48],"prior":[51],"participating":[53],"CASP6.":[55,112],"additionally":[57],"tested":[58],"new":[59],"ideas":[60],"amenable":[63],"full-automation":[65],"with":[66,103],"an":[67],"eye":[68],"toward":[69],"improving":[70],"server.":[72],"find":[74],"shows":[79],"greatest":[81],"promise":[82],"more":[85],"challenging":[86],"most":[89],"significant":[90],"finding":[91],"from":[92],"CASP5,":[93],"automated":[95],"can":[97],"be":[98],"roughly":[99],"comparable":[100],"ability":[102],"better":[105],"human-intervention":[106],"predictors,":[107],"repeated":[109],"here":[110]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":7}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}