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Proteins. 2011;79 Suppl 10:161-71. doi: 10.1002/prot.23175. Epub 2011 Oct 11.

RaptorX: exploiting structure information for protein alignment by statistical inference.

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  • 1Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL 60637, USA.


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

Copyright © 2011 Wiley-Liss, Inc.

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