{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T04:13:24Z","timestamp":1778732004337,"version":"3.51.4"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: In recent years, development of a single-method fold-recognition server lags behind consensus and multiple template techniques. However, a good consensus prediction relies on the accuracy of individual methods. This article reports our efforts to further improve a single-method fold recognition technique called SPARKS by changing the alignment scoring function and incorporating the SPINE-X techniques that make improved prediction of secondary structure, backbone torsion angle and solvent accessible surface area.<\/jats:p>\n               <jats:p>Results: The new method called SPARKS-X was tested with the SALIGN benchmark for alignment accuracy, Lindahl and SCOP benchmarks for fold recognition, and CASP 9 blind test for structure prediction. The method is compared to several state-of-the-art techniques such as HHPRED and BoostThreader. Results show that SPARKS-X is one of the best single-method fold recognition techniques. We further note that incorporating multiple templates and refinement in model building will likely further improve SPARKS-X.<\/jats:p>\n               <jats:p>Availability: The method is available as a SPARKS-X server at http:\/\/sparks.informatics.iupui.edu\/<\/jats:p>\n               <jats:p>Contact: \u00a0yqzhou@iupui.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr350","type":"journal-article","created":{"date-parts":[[2011,6,12]],"date-time":"2011-06-12T00:35:05Z","timestamp":1307838905000},"page":"2076-2082","source":"Crossref","is-referenced-by-count":292,"title":["Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates"],"prefix":"10.1093","volume":"27","author":[{"given":"Yuedong","family":"Yang","sequence":"first","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eshel","family":"Faraggi","sequence":"additional","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiying","family":"Zhao","sequence":"additional","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yaoqi","family":"Zhou","sequence":"additional","affiliation":[{"name":"1 School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202 and 2Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA"},{"name":"1 School of Informatics, Indiana University Purdue University, 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