ILRI Research Computing

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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.

[[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/
<file>
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.

</file>
Running FIEFDom
<code>FIEFDom<WIN/LIN>.exe <input.fasta></code>


 	
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