{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:13Z","timestamp":1740185113007,"version":"3.37.3"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T00:00:00Z","timestamp":1597104000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["5U01 GM093324-02"],"award-info":[{"award-number":["5U01 GM093324-02"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Methods to assess the quality of protein structure models are needed for user applications. To aid with the selection of structure models and further inform the development of structure prediction techniques, we describe the ResiRole method for the assessment of the quality of structure models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Structure prediction techniques are ranked according to the results of round-robin, head-to-head comparisons using difference scores. Each difference score was defined as the absolute value of the cumulative probability for a functional site prediction made with the FEATURE program for the reference structure minus that for the structure model. Overall, the difference scores correlate well with other model quality metrics; and based on benchmarking studies with Na\u00efveBLAST, they are found to detect additional local structural similarities between the structure models and reference structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>Automated analyses of models addressed in CAMEO are available via the ResiRole server, URL http:\/\/protein.som.geisinger.edu\/ResiRole\/. Interactive analyses with user-provided models and reference structures are also enabled. Code is available at github.com\/wamclaughlin\/ResiRole.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa712","type":"journal-article","created":{"date-parts":[[2020,8,5]],"date-time":"2020-08-05T19:31:54Z","timestamp":1596655914000},"page":"351-359","source":"Crossref","is-referenced-by-count":1,"title":["ResiRole: residue-level functional site predictions to gauge the accuracies of protein structure prediction techniques"],"prefix":"10.1093","volume":"37","author":[{"given":"Joshua M","family":"Toth","sequence":"first","affiliation":[{"name":"Geisinger Commonwealth School of Medicine Department of Medical Education, , Scranton, PA 18510, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul J","family":"DePietro","sequence":"additional","affiliation":[{"name":"Geisinger Commonwealth School of Medicine Department of Medical Education, , Scranton, PA 18510, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juergen","family":"Haas","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics , CH-4056 Basel, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9234-9418","authenticated-orcid":false,"given":"William A","family":"McLaughlin","sequence":"additional","affiliation":[{"name":"Geisinger Commonwealth School of Medicine Department of Medical Education, , Scranton, PA 18510, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,8,11]]},"reference":[{"key":"2023051604084943400_btaa712-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023051604084943400_btaa712-B2","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1126\/science.1065659","article-title":"Protein structure prediction and structural genomics","volume":"294","author":"Baker","year":"2001","journal-title":"Science"},{"key":"2023051604084943400_btaa712-B3","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2023051604084943400_btaa712-B4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023051604084943400_btaa712-B5","doi-asserted-by":"crossref","first-page":"1851","DOI":"10.1093\/bioinformatics\/bts292","article-title":"Improvement of 3D protein models using multiple templates guided by single-template model quality assessment","volume":"28","author":"Buenavista","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051604084943400_btaa712-B6","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41598-017-00919-w","article-title":"Assembly of Ruminococcus flavefaciens cellulosome revealed by structures of two cohesin\u2013dockerin complexes","volume":"7","author":"Bule","year":"2017","journal-title":"Sci. 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