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PSPP - A Protein Structure Prediction Pipeline for Computing Clusters
Protein structures are critical for understanding the mechanisms of biological systems and, subsequently, for drug and vaccine design. Unfortunately, protein sequence data exceed structural data by a factor of more than 200 to 1. This gap can be partially filled by using computational protein structure prediction. While structure prediction Web servers are a notable option, they often restrict the number of sequence queries and/or provide a limited set of prediction methodologies. Therefore, we present a standalone protein structure prediction software package suitable for high-throughput structural genomic applications that performs all three classes of prediction methodologies: comparative modeling, fold recognition, and ab initio. This software can be deployed on a user's own high-performance computing cluster.
sspro : http://download.igb.uci.edu/
FIEFDom : http://www.bhsai.org/downloads/fiefdom/
Edit the paths in 'configure.txt' (in the 'data' folder) for the platform on which the program is being run. BLASTPGP - should point to the 'bin' directory (including the '\' or '/' in the end) containing the 'blastpgp' executable. DATABASE- should point to the name of the BLAST parseable database.