{"id":"https://openalex.org/W2946278656","doi":"https://doi.org/10.1093/nar/gkz402","title":"PSICA: a fast and accurate web service for protein model quality analysis","display_name":"PSICA: a fast and accurate web service for protein model quality analysis","publication_year":2019,"publication_date":"2019-05-02","ids":{"openalex":"https://openalex.org/W2946278656","doi":"https://doi.org/10.1093/nar/gkz402","mag":"2946278656","pmid":"https://pubmed.ncbi.nlm.nih.gov/31127307"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz402","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W443/28880278/gkz402.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","license_id":"https://openalex.org/licenses/cc-by","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/47/W1/W443/28880278/gkz402.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100350662","display_name":"Wenbo Wang","orcid":"https://orcid.org/0000-0001-8275-1067"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenbo Wang","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0001-8275-1067","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065454135","display_name":"Zhaoyu Li","orcid":"https://orcid.org/0000-0001-6223-5639"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhaoyu Li","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101617584","display_name":"Junlin Wang","orcid":"https://orcid.org/0000-0002-7331-3580"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junlin Wang","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082428303","display_name":"Dong Xu","orcid":"https://orcid.org/0000-0002-4809-0514"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dong Xu","raw_affiliation_strings":["Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA","Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057883374","display_name":"Yi Shang","orcid":"https://orcid.org/0000-0001-7771-4034"},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yi Shang","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA"],"raw_orcid":"https://orcid.org/0000-0001-7771-4034","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5057883374"],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.6629,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.67786452,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"47","issue":"W1","first_page":"W443","last_page":"W450"},"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":0.9988999962806702,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9962999820709229,"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/rendering","display_name":"Rendering (computer graphics)","score":0.5936819911003113},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5929794311523438},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5008795261383057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4996826648712158},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4472264051437378},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4166533946990967},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.356692373752594},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20645856857299805},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1519678235054016}],"concepts":[{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.5936819911003113},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5929794311523438},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5008795261383057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4996826648712158},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4472264051437378},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4166533946990967},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.356692373752594},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20645856857299805},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1519678235054016}],"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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkz402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz402","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W443/28880278/gkz402.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:31127307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31127307","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:europepmc.org:5577254","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602450","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz402","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W443/28880278/gkz402.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G4041811226","display_name":null,"funder_award_id":"R01 GM100700","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5427449508","display_name":null,"funder_award_id":"R01-GM100701","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7585683335","display_name":null,"funder_award_id":"R35 GM126985","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7975266290","display_name":null,"funder_award_id":"R35-GM126985","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1940137454","https://openalex.org/W1965615878","https://openalex.org/W1998676514","https://openalex.org/W1999613945","https://openalex.org/W2093567555","https://openalex.org/W2096339761","https://openalex.org/W2103986334","https://openalex.org/W2115540209","https://openalex.org/W2116672918","https://openalex.org/W2119068667","https://openalex.org/W2125677968","https://openalex.org/W2126711803","https://openalex.org/W2143210482","https://openalex.org/W2145268834","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2168321064","https://openalex.org/W2418704427","https://openalex.org/W2559617060","https://openalex.org/W2565608178","https://openalex.org/W2609811411","https://openalex.org/W2616930327","https://openalex.org/W2748374366","https://openalex.org/W2899950364"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2070401501","https://openalex.org/W2121496884","https://openalex.org/W2387910809"],"abstract_inverted_index":{"This":[0],"paper":[1],"presents":[2],"a":[3,29,33,100,144],"new":[4,145],"fast":[5],"and":[6,48,92,118,133,168,178,188],"accurate":[7],"web":[8],"service":[9],"for":[10,185],"protein":[11,35,42,46,55,65,79,121],"model":[12,31,66,80,117,160,184],"quality":[13,52,67,129],"analysis,":[14],"called":[15],"PSICA":[16,57,105,141,193],"(Protein":[17],"Structural":[18],"Information":[19],"Conformity":[20],"Analysis).":[21],"It":[22],"is":[23,195],"designed":[24],"to":[25,39,49],"evaluate":[26,50],"how":[27],"much":[28],"tertiary":[30],"of":[32,44,53,86,96,125,130,137,182],"given":[34,101],"primary":[36],"sequence":[37],"conforms":[38],"the":[40,51,59,78,87,90,116,126,131,138,164,172,176],"known":[41,120],"structures":[43],"similar":[45],"sequences,":[47],"predicted":[54,91,102,108,127,177],"models.":[56],"implements":[58,142],"MUfoldQA_S":[60,73],"method,":[61],"an":[62],"efficient":[63],"state-of-the-art":[64],"assessment":[68],"(QA)":[69],"method.":[70],"In":[71,151],"CASP12,":[72,152],"ranked":[74,154],"No.":[75,155,169],"1":[76,156,159],"in":[77,84,157,171],"QA":[81,166,190],"select-20":[82,165,187],"category":[83,167],"terms":[85],"difference":[88,174],"between":[89,115,175],"true":[93,179],"GDT-TS":[94,110,161,180],"value":[95,181],"each":[97,183],"model.":[98,139],"For":[99],"3D":[103],"model,":[104],"generates":[106],"(i)":[107],"global":[109],"value;":[111],"(ii)":[112],"interactive":[113],"comparison":[114],"other":[119],"structures;":[122],"(iii)":[123],"visualization":[124],"local":[128],"model;":[132],"(iv)":[134],"JSmol":[135],"rendering":[136],"Additionally,":[140],"MUfoldQA_C,":[143],"consensus":[146],"method":[147],"based":[148],"on":[149,163],"MUfoldQA_S.":[150],"MUfoldQA_C":[153],"top":[158],"loss":[162],"2":[170],"average":[173],"both":[186],"best-150":[189],"categories.":[191],"The":[192],"server":[194],"freely":[196],"available":[197],"at":[198],"http://qas.wangwb.com/\u223cwwr34/mufoldqa/index.html.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
