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pspp [2009/11/09 12:53] – created 172.26.0.166pspp [2010/05/22 14:19] (current) – external edit 127.0.0.1
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 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. 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://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0006254;jsessionid=FAFDBB60D6EF54E714F6B66FFF8B0FF7]]+[[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
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