pspro: a suite of protems to predict protein 1D and 2D structure featuers (secondary structure, solvent
accessibility, contact map).

Free for academic use only.
All rights reserved.

Author:

Jianlin Cheng
Department of Computer Science
University of Missouri, Columbia
Email: chengji@missouri.edu

Reference:

1. J. Cheng, A. Randall, M. Sweredoski, and P. Baldi, SCRATCH: a Protein
Structure and Structural Feature Prediction Server.
Nucleic Acids Research, vol. 33 (web server issue), w72-76, 2005.

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Installation:

open configure.pl

set $install_dir to the directory of prosys

save the file.

run configure.pl to configure it.

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1. predict_ss_sa_cm.pl fasta_file output_dir

predict the secondary structure, solvent accessibility, and contacct map for
one single sequence in fasta_file
output files are stored in output_dir.

This script uses only ab initio methods.

Test:

cd ./test
../bin/predict_ss_sa_cm.pl 1aqta.fasta ./out

The results in out should be the same as in ./1aqta.

2. predict_homo_cm.pl fasta.file output_dir

predict the secondary structure, solvent accessibility, and contacct map for
one single sequence in fasta_file
output files are stored in output_dir.

This script uses only both ab initio and homology methods.

Test:

cd ./test
../bin/predict_ss_sa_cm.pl 1aqta.fasta ./out

The results in out should be the same as in ./1aqta_homo.