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.
abstract: BACKGROUND
  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.
  
  
  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.
  
  
  BACKGROUND
  The method is available as a SPARKS-X server at http://sparks.informatics.iupui.edu/
authors.affiliation: School of Informatics, Indiana University Purdue University, Indianapolis, IN 46202, USA.
authors.forename: Yuedong
authors.initials: Y
authors.lastname: Yang
authors.forename: Eshel
authors.initials: E
authors.lastname: Faraggi
authors.forename: Huiying
authors.initials: H
authors.lastname: Zhao
authors.forename: Yaoqi
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins