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.

http://ukpmc.ac.uk/articlerender.cgi?tool=pubmed&pubmedid=19606223

DISPRO/SSPRO

Dispro : http://download.igb.uci.edu/intro.html#5

sspro : http://download.igb.uci.edu/

PRODIV-TMHMM :

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.


Change the file permissions of the executable by running  'chmod FEIFDomLIN.exe 755' for
  the Linux version.

Running FIEFDom 

FIEFDom<WIN/LIN>.exe <input.fasta>

Rosetta and PyRosetta Software

Rosetta Software Logo from Baker Laboratory

Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions. The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.

./prospect_ssp.LINUX -prospect_path /home/magochi/src/PSPP/pspp_1.0/prospect/prospect -seqfile /home/magochi/seq.fasta