{"id":"https://openalex.org/W2166867047","doi":"https://doi.org/10.1093/bioinformatics/bti249","title":"PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY","display_name":"PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY","publication_year":2005,"publication_date":"2005-01-12","ids":{"openalex":"https://openalex.org/W2166867047","doi":"https://doi.org/10.1093/bioinformatics/bti249","mag":"2166867047","pmid":"https://pubmed.ncbi.nlm.nih.gov/15647301"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/277/50305607/bioinformatics_21_3_277.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/21/3/277/50305607/bioinformatics_21_3_277.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015217651","display_name":"Alfonso Valencia","orcid":"https://orcid.org/0000-0002-8937-6789"},"institutions":[{"id":"https://openalex.org/I4210104776","display_name":"Centro Nacional de Biotecnolog\u00eda","ror":"https://ror.org/015w4v032","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210104776"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Alfonso Valencia","raw_affiliation_strings":["Protein Design Group Centro Nacional de Biotecnologia-CSIC Darwin 3, Cantoblanco, Madrid 28049, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Protein Design Group Centro Nacional de Biotecnologia-CSIC Darwin 3, Cantoblanco, Madrid 28049, Spain","institution_ids":["https://openalex.org/I4210104776"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5015217651"],"corresponding_institution_ids":["https://openalex.org/I4210104776"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":1.7729,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.84080476,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"3","first_page":"277","last_page":"277"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9627000093460083,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9627000093460083,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9578999876976013,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9549000263214111,"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/casp","display_name":"CASP","score":0.9760211706161499},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6143564581871033},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5152266621589661},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4927826225757599},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.38460421562194824},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.37432509660720825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3340752124786377},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1605280041694641}],"concepts":[{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.9760211706161499},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6143564581871033},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5152266621589661},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4927826225757599},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.38460421562194824},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.37432509660720825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3340752124786377},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1605280041694641}],"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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008967","descriptor_name":"Molecular Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/277/50305607/bioinformatics_21_3_277.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:15647301","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15647301","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":"Editorial"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti249","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti249","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/3/277/50305607/bioinformatics_21_3_277.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":[{"id":"https://metadata.un.org/sdg/2","score":0.6399999856948853,"display_name":"Zero hunger"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2166867047.pdf","grobid_xml":"https://content.openalex.org/works/W2166867047.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W2141022852"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2147472674","https://openalex.org/W2561391236","https://openalex.org/W1888349473","https://openalex.org/W2136856901","https://openalex.org/W3165545667","https://openalex.org/W4225106352","https://openalex.org/W47248631","https://openalex.org/W3171039768","https://openalex.org/W2058542300"],"abstract_inverted_index":{"The":[0,287],"CASP":[1,46,79,152,288,320],"community-wide":[2],"assessment":[3],"of":[4,18,63,91,105,132,144,180,199,204,216,255,263,319],"protein":[5,29,39,226],"structure":[6,30,40,96,104,227,262],"prediction":[7,31,41,228],"methods":[8,42,134,200,229],"(CASP6,":[9],"2004,":[10],"http://predictioncenter.llnl.gov/casp6/)":[11],"anniversary":[12],"coincides":[13],"with":[14,275],"a":[15,83,222,264,271,282,292],"general":[16],"realization":[17],"the":[19,33,77,89,92,103,115,129,141,145,178,181,197,202,261,279,302,308,317],"need":[20],"to":[21,95,120,128,140,169,193,196,258,316],"speed":[22],"progress,":[23],"and":[24,155],"achieve":[25],"sustained":[26],"success":[27],"in":[28,60,88,177,238,243,246,278,295],"[see":[32],"NIGMS-NIH":[34],"new":[35,69,130,299],"initiative":[36],"for":[37,99,150,201,224,231,270],"improving":[38],"(http://www.nigms.nih.gov/)],":[43],"toward":[44],"which":[45,113],"has":[47,54,81,290],"substantially":[48,259],"contributed.":[49],"Unfortunately,":[50],"so":[51],"far":[52],"progress":[53,87,165],"not":[55,125,167],"been":[56],"as":[57,59,110,148,321],"continuous":[58],"other":[61],"fields":[62],"technology,":[64],"perhaps":[65],"indicating":[66,187],"that":[67,163,188,266],"substantial":[68,86,189],"scientific":[70],"contribu-":[71],"tions":[72],"are":[73],"still":[74],"required.":[75],"Interestingly,":[76],"recent":[78],"edition":[80],"shown":[82,149,291],"small":[84],"but":[85,138,301],"quality":[90,179],"corresponding":[93],"sequence":[94,146],"alignments,":[97,186],"particularly":[98,160],"modeling":[100],"based":[101],"on":[102],"similar":[106],"proteins":[107],"(commonly":[108],"known":[109],"homology":[111],"modeling),":[112],"is":[114,124,159,162],"area":[116],"most":[117],"directly":[118,171,296],"applicable":[119],"biology.":[121,232],"This":[122],"improvement":[123,176],"only":[126],"related":[127],"generation":[131],"sequence-based":[133],"(e.g.":[135],"profile\u2013profile":[136],"alignments),":[137],"also":[139],"pure":[142],"growth":[143],"databases,":[147],"previous":[151],"editions":[153],"(Cozzetto":[154],"Tramontano,":[156],"2005).":[157],"What":[158],"interesting":[161,314],"this":[164,208,298],"does":[166],"seem":[168],"be":[170,194,211,242],"followed":[172],"by":[173,307],"an":[174,313],"obvious":[175],"models":[182],"derived":[183],"from":[184],"those":[185],"work":[190],"would":[191,219],"have":[192,236],"dedicated":[195],"development":[198],"refinement":[203,213,309],"structural":[205],"models.":[206],"If":[207],"tendency":[209],"can":[210],"confirmed,":[212],"after":[214],"identification":[215],"sequence\u2013structure":[217],"alignment":[218],"soon":[220],"become":[221],"bottleneck":[223],"making":[225],"useful":[230],"From":[233],"what":[234],"we":[235],"seen":[237],"CASP6,":[239],"solutions":[240],"may":[241],"reach,":[244],"e.g.":[245],"at":[247],"least":[248],"one":[249],"case":[250],"David":[251],"Baker's":[252],"group":[253],"(University":[254],"Washington)":[256],"managed":[257],"improve":[260],"model,":[265],"they":[267],"had":[268],"built":[269],"very":[272],"difficult":[273],"protein,":[274],"no":[276],"homologs":[277],"database,":[280],"using":[281],"standard":[283],"full-atom":[284],"force":[285],"field.":[286],"community":[289],"genuine":[293],"interest":[294],"addressing":[297],"challenge,":[300],"specific":[303],"computational":[304],"demands":[305],"required":[306],"programs":[310],"certainly":[311],"pose":[312],"challenge":[315],"organization":[318],"it":[322],"enters":[323],"its":[324],"second":[325],"decade.":[326]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2025-10-10T00:00:00"}
