title: RaptorX: exploiting structure information for protein alignment by statistical inference.
abstract: This work presents RaptorX, a statistical method for template-based protein modeling that improves alignment accuracy by exploiting structural information in a single or multiple templates. RaptorX consists of three major components: single-template threading, alignment quality prediction, and multiple-template threading. This work summarizes the methods used by RaptorX and presents its CASP9 result analysis, aiming to identify major bottlenecks with RaptorX and template-based modeling and hopefully directions for further study. Our results show that template structural information helps a lot with both single-template and multiple-template protein threading especially when closely-related templates are unavailable, and there is still large room for improvement in both alignment and template selection. The RaptorX web server is available at http://raptorx.uchicago.edu.
authors: Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL 60637, USA.
authors: Jian
authors: J
authors: Peng
authors: Jinbo
authors: J
authors: Xu
mesh_terms: D000465:Algorithms; D001699:Biometry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D011506:Proteins