{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T18:49:04Z","timestamp":1767034144332,"version":"3.37.3"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2021,7,11]],"date-time":"2021-07-11T00:00:00Z","timestamp":1625961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Robert J. Mattauch Endowment"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>X-ray crystallography was used to produce nearly 90% of protein structures. These efforts were supported by numerous sequence-based tools that accurately predict crystallizable proteins. However, protein structures vary widely in their quality, typically measured with resolution and R-free. This impacts the ability to use these structures for some applications including rational drug design and molecular docking and motivates development of methods that accurately predict structure quality from sequence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce XRRpred, the first predictor of the resolution and R-free values from protein sequences. XRRpred relies on original sequence profiles, hand-crafted features, empirically selected and parametrized regressors and modern resampling techniques. Using an independent test dataset, we show that XRRpred provides accurate predictions of resolution and R-free. We demonstrate that XRRpred\u2019s predictions correctly model relationship between the resolution and R-free and reproduce structure quality relations between structural classes of proteins. We also show that XRRpred significantly outperforms indirect alternative ways to predict the structure quality that include predictors of crystallization propensity and an alignment-based approach. XRRpred is available as a convenient webserver that allows batch predictions and offers informative visualization of the results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/biomine.cs.vcu.edu\/servers\/XRRPred\/.<\/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\/btab509","type":"journal-article","created":{"date-parts":[[2021,7,6]],"date-time":"2021-07-06T19:12:38Z","timestamp":1625598758000},"page":"4366-4374","source":"Crossref","is-referenced-by-count":9,"title":["XRRpred: accurate predictor of crystal structure quality from protein sequence"],"prefix":"10.1093","volume":"37","author":[{"given":"Sina","family":"Ghadermarzi","sequence":"first","affiliation":[{"name":"Department of Computer Science, Virginia Commonwealth University , Richmond, VA 23284, USA"}]},{"given":"Bartosz","family":"Krawczyk","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Virginia Commonwealth University , Richmond, VA 23284, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8031-9086","authenticated-orcid":false,"given":"Jiangning","family":"Song","sequence":"additional","affiliation":[{"name":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia"},{"name":"Monash Centre for Data Science, Faculty of Information Technology, Monash University , Melbourne, VIC 3800, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7749-0314","authenticated-orcid":false,"given":"Lukasz","family":"Kurgan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Virginia Commonwealth University , Richmond, VA 23284, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,7,11]]},"reference":[{"key":"2023061310471930200_btab509-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"},{"year":"2011","author":"Bach","key":"2023061310471930200_btab509-B2"},{"first-page":"193","year":"2019","author":"Branco","key":"2023061310471930200_btab509-B3"},{"key":"2023061310471930200_btab509-B4","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/j.neucom.2018.11.100","article-title":"Pre-processing approaches for imbalanced distributions in regression","volume":"343","author":"Branco","year":"2019","journal-title":"Neurocomputing"},{"volume-title":"Classification and Regression Trees","year":"1984","author":"Breiman","key":"2023061310471930200_btab509-B5"},{"key":"2023061310471930200_btab509-B6","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1038\/355472a0","article-title":"Free R value: a novel statistical quantity for assessing the accuracy of crystal structures","volume":"355","author":"Brunger","year":"1992","journal-title":"Nature"},{"key":"2023061310471930200_btab509-B7","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/d41586-020-01658-1","article-title":"\u2018It opens up a whole new universe\u2019: revolutionary microscopy technique sees individual atoms for first time","volume":"582","author":"Callaway","year":"2020","journal-title":"Nature"},{"key":"2023061310471930200_btab509-B8","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1016\/j.jmb.2004.09.076","article-title":"Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics","volume":"344","author":"Canaves","year":"2004","journal-title":"J. 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