{"id":"https://openalex.org/W2130259216","doi":"https://doi.org/10.1093/nar/gki403","title":"PROTINFO: new algorithms for enhanced protein structure predictions","display_name":"PROTINFO: new algorithms for enhanced protein structure predictions","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2130259216","doi":"https://doi.org/10.1093/nar/gki403","mag":"2130259216","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980581"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki403","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W77/7622872/gki403.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/33/suppl_2/W77/7622872/gki403.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012172477","display_name":"Ling\u2010Hong Hung","orcid":"https://orcid.org/0000-0002-5209-2248"},"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":true,"raw_author_name":"L.-H. Hung","raw_affiliation_strings":["Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA","Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044183859","display_name":"Shing-Chung Ngan","orcid":"https://orcid.org/0000-0002-8160-2454"},"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":"S.-C. Ngan","raw_affiliation_strings":["Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102959085","display_name":"Tianyun Liu","orcid":null},"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":"T. Liu","raw_affiliation_strings":["Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059358345","display_name":"Ram Samudrala","orcid":"https://orcid.org/0000-0001-9069-8497"},"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":"R. Samudrala","raw_affiliation_strings":["Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Group, Department of Microbiology, University of Washington School of Medicine  Seattle, WA 98195, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5012172477"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":3.8932,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.94158919,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"33","issue":"Web Server","first_page":"W77","last_page":"W80"},"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":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9923999905586243,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7659834623336792},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.7395464181900024},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5540049076080322},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5476060509681702},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.5414599776268005},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5007710456848145},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4995884895324707},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4564847946166992},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36156922578811646},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35205256938934326},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3168003261089325},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17584341764450073},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11860522627830505},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09400048851966858}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7659834623336792},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.7395464181900024},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5540049076080322},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5476060509681702},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.5414599776268005},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5007710456848145},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4995884895324707},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4564847946166992},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36156922578811646},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35205256938934326},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3168003261089325},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17584341764450073},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11860522627830505},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09400048851966858}],"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":"D008958","descriptor_name":"Models, Molecular","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gki403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki403","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W77/7622872/gki403.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980581","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980581","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:CiteSeerX.psu:10.1.1.594.2793","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.594.2793","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/33/suppl_2/W77.full-text-lowres.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:1316335","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC1160164","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1160164","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160164","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/gki403","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki403","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W77/7622872/gki403.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5498590512","display_name":"Modelling Structure and Function of Proteins Encoded by the Rice Genome","funder_award_id":"0217241","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6575694142","display_name":null,"funder_award_id":"R33 GM068152","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7786465035","display_name":null,"funder_award_id":"GM068152","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310094","display_name":"University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130259216.pdf","grobid_xml":"https://content.openalex.org/works/W2130259216.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1491468287","https://openalex.org/W1990367639","https://openalex.org/W2038335203","https://openalex.org/W2085950396","https://openalex.org/W2097651746","https://openalex.org/W2099148717","https://openalex.org/W2100116869","https://openalex.org/W2101207060","https://openalex.org/W2116007667","https://openalex.org/W2117898940","https://openalex.org/W2118942240","https://openalex.org/W2125176038","https://openalex.org/W2134455806","https://openalex.org/W2141783940","https://openalex.org/W2143288492","https://openalex.org/W2143366433","https://openalex.org/W2155350790","https://openalex.org/W2161776897","https://openalex.org/W2164750034","https://openalex.org/W3145015749","https://openalex.org/W3201606613","https://openalex.org/W4230638849","https://openalex.org/W4247866849","https://openalex.org/W4250437674","https://openalex.org/W4250753748","https://openalex.org/W4376043833"],"related_works":["https://openalex.org/W2221737924","https://openalex.org/W1995553782","https://openalex.org/W2345242111","https://openalex.org/W1020920971","https://openalex.org/W2130259216","https://openalex.org/W3118344282","https://openalex.org/W63398591","https://openalex.org/W3193795503","https://openalex.org/W4232483067","https://openalex.org/W2098405947"],"abstract_inverted_index":{"We":[0,47],"describe":[1],"new":[2],"algorithms":[3,29],"and":[4,21,81],"modules":[5,72],"for":[6],"protein":[7,79],"structure":[8,88],"prediction":[9],"available":[10,96],"as":[11],"part":[12],"of":[13,42,50,89],"the":[14,35,39,61,86],"PROTINFO":[15,93],"web":[16],"server.":[17],"The":[18,92],"modules,":[19],"comparative":[20],"de":[22],"novo":[23],"modelling,":[24],"have":[25],"significantly":[26],"improved":[27],"back-end":[28],"that":[30,90],"were":[31,48],"rigorously":[32],"evaluated":[33],"at":[34,97],"sixth":[36],"meeting":[37],"on":[38],"Critical":[40],"Assessment":[41],"Protein":[43],"Structure":[44],"Prediction":[45],"methods.":[46],"one":[49],"four":[51],"server":[52,94],"groups":[53,64],"invited":[54],"to":[55,67,76],"make":[56],"an":[57],"oral":[58],"presentation":[59],"(only":[60],"best":[62],"performing":[63],"are":[65],"asked":[66],"do":[68],"so).":[69],"These":[70],"two":[71],"allow":[73],"a":[74,78],"user":[75],"submit":[77],"sequence":[80],"return":[82],"atomic":[83],"coordinates":[84],"representing":[85],"tertiary":[87],"protein.":[91],"is":[95],"http://protinfo.compbio.washington.edu.":[98]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":2}],"updated_date":"2026-03-11T06:11:40.159057","created_date":"2025-10-10T00:00:00"}
