Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 79, Issue -, Pages 161-171Publisher
WILEY
DOI: 10.1002/prot.23175
Keywords
single-template threading; multiple-template threading; alignment quality prediction; probabilistic alignment; multiple protein alignment; CASP
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Funding
- National Institutes of Health [R01GM089753]
- National Science Foundation [DBI-0960390]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM089753] Funding Source: NIH RePORTER
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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. Proteins 2011; 79(Suppl 10): 161-171. (C) 2011 Wiley-Liss, Inc.
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