Prospect version 0.92

Prospect:: is an application programmer interface (API) to the PROSPECT Pro threading application. The modules provide for program execution, results parsing, multiple sequence alignments inferred from pairwise sequence-structure alignments, and rudimentary homology models.

For more information on PROSPECT Pro:
Kim, D., Xu, D., Guo, J., Ellrott, K. and Xu, Y. (2003) PROSPECT II: Protein structure prediction method for genome-scale applications. Protein Eng., 16(9), 641-50. Commercial versions available from Bioinformatics Solutions, Inc. (http://www.bioinformaticssolutions.com/).

INSTALLATION

To install this module type the following:

perl Makefile.PL
make

<configure the Prospect::Init module> make test
make install

CONFIGURATION

After installation,
1) configure the Prospect::Init module with your system specifics. 2) run the bin/processPdbFiles script to generate processed PDB files. These processed files are necessary for generating rudimentary backbone-only homology models in PDB format by mapping the aligned residues onto the 3D template. Make sure that you have defined the PROSPECT_PATH, PDB_PATH, and PROCESSED_PDB_PATH variables correctly within the Prospect::Init module.

Something akin to this bash command will build all of processed PDB files.

        export PROSPECT_PATH=<top-level of your prospect install>;
        find $PROSPECT_PATH -name \.xml | 
        sed -e 's/^.\///;s/\.xml$//' | 
        xargs perl -I ../.. processPdbFiles

DEPENDENCIES
This module requires these other modules and libraries:

XML::Parser, XML::Simple, Digest::MD5 (available from http://www.cpan.org) and bioperl (http://www.bioperl.org).
For remote threading, SOAP::Lite (http://www.soaplite.com/) and SOAP::Transport::HTTP::Daemon (http://www.cpan.org) are required.
Colorized multiple sequence alignments requires mview (http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/).
Viewing sequence-structure alignments requires rasmol (http://www.openrasmol.org/).

AUTHORS
David S. Cavanaugh (cavs@gene.com) and Reece K. Hart (rkh@gene.com)

FOR MORE INFORMATION

see http://share.gene.com