title: Local protein structure prediction using discriminative models.
abstract: BACKGROUND
  In recent years protein structure prediction methods using local structure information have shown promising improvements. The quality of new fold predictions has risen significantly and in fold recognition incorporation of local structure predictions led to improvements in the accuracy of results. We developed a local structure prediction method to be integrated into either fold recognition or new fold prediction methods. For each local sequence window of a protein sequence the method predicts probability estimates for the sequence to attain particular local structures from a set of predefined local structure candidates. The first step is to define a set of local structure representatives based on clustering recurrent local structures. In the second step a discriminative model is trained to predict the local structure representative given local sequence information.
  
  
  RESULTS
  The step of clustering local structures yields an average RMSD quantization error of 1.19 A for 27 structural representatives (for a fragment length of 7 residues). In the prediction step the area under the ROC curve for detection of the 27 classes ranges from 0.68 to 0.88.
  
  
  CONCLUSIONS
  The described method yields probability estimates for local protein structure candidates, giving signals for all kinds of local structure. These local structure predictions can be incorporated either into fold recognition algorithms to improve alignment quality and the overall prediction accuracy or into new fold prediction methods.
authors.affiliation: Max-Planck-Institute for Informatics, Department of Computational Biology and Applied Algorithmics, Stuhlsatzenhausweg 85, D-66123 Saarbrücken, Germany. osander@mpi-sb.mpg.de
authors.forename: Oliver
authors.initials: O
authors.lastname: Sander
authors.forename: Ingolf
authors.initials: I
authors.lastname: Sommer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lengauer
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D003198:Computer Simulation; D016002:Discriminant Analysis; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated / Q000379:methods*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins