SVMcon is a software to predict protein residue-residue contacts in 8 Angstrom distance threshold.
It is one of the most accurate contact predictors in the 7th and 8th editions of Critical Assessment of Techniques for Protein Structure Prediction (CASP7&8).
It is the only free contact map prediction software (including source code) available so far.

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Installation

1. install secondary structure and solvent accessibility predictor PSpro (PSpro1.1 or PSpro2.0) (download it from: http://sysbio.rnet.missouri.edu/multicom_toolbox/. easy to install).

2. unzip svmcon.tar.gz

3. do configuration

cd svmcon
open configure.pl
set $install_dir to svmcon directory
set $pspro_dir to PSpro directory (full path)
save configure.pl
run ./configure.pl to configure.

installation is done.

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Test Installation

cd test
../bin/predict_map.sh T0288.fasta test.map??

The output test.map should be the same as T0288.map.final

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Run the program:

predict_map.sh fasta_file output_file

fasta_file: protein sequence in the simple FASTA foramt
(line1: >name; line 2: a plain protein sequence).

Output file includes the predicted residue contacts in CASP format.

Notice:
Since there are lot of support vectors in the SVM model, it takes from
tens of minutes to several hours to predict contacts for a protein, depending
on sequence length.

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Reference:

J. Cheng and P. Baldi. Improved Residue Contact Prediction Using Support Vector Machines and a Large Feature Set. BMC Bioinformatics. 8:113, 2007.

Author: Jianlin Cheng, PhD. School of EECS, University of Central Florida.

Free for academic and scientific use only.
Copyright @ Jianlin Cheng
Please do not re-distribute the software without the permission of the author.

Contact:
Jianlin Cheng at chengji@missouri.edu

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Third-party software used by SVMcon

SVMcon softwre uses svm_classify program in SVM-light (svmlight.joachims.org) to classify data points.

Reference to SVM-light:

T. Joachims, 11 in: Making large-Scale SVM Learning Practical. Advances in Kernel Methods - Support Vector Learning, B. Sch?lkopf and C. Burges and A. Smola (ed.), MIT Press, 1999.

I thank the author of SVM-light (Dr. Thorsten Joachims) for the permit to include svm_classify in the SVMcon package.

Here is the license quoted from the SVM-light website:

SVM-light is free only for non-commercial use. It must not be distributed without prior permission of the author. The author is not responsible for implications from the use of this software.