DIpro 2.0: Prediction of disulfide bonds from protein sequences

References:
[1] J. Cheng, H. Saigo, P. Baldi, "Large-Scale Prediction of
Disulphide Bridges Using Kernel Methods, Two-Dimensional Recursive Neural
Networks, and Weighted Graph Matching". Proteins: Structure, Function, Bioinformatics, vol 62, no. 3, pp. 617-629, 2006. 
[2] P. Baldi, J. Cheng, A. Vullo, Large-Scale Prediction of Disulphide Bond Connectivity , 
Advances in Neural Information Processing Systems (NIPS 2004) 17, 
L. Saul,Y. Weiss, and L. Bottou editors, MIT press, pp.97-104, Cambridge, MA, 2005.

Contact:
Jianlin Cheng
Ph.D. candidate
School of Information and Computer Sciences
University of California Irvine
email: jianlinc@uci.edu

Copyright: 
	Free for academic/scientific use. 


Installation (Linux Version):

0. Install SSpro4.0 package first. Get it from: http://contact.ics.uci.edu/download.html. 
	Very easy to install. 

1.unzip dipro2.0.tar.gz
	e.g. tar xzf  dipro2.0.tar.gz

2.change directory into dipro2.0
	e.g. cd dipro2.0

3. edit configure.pl
	set DIpro path ($install_dir) and SSpro4 path ($pspro_dir) to their installation directories.

4. run configure.pl
	e.g. ./configure.pl

Installation is done.

Check the integrity of installation
	cd test
	../bin/predict_disu.sh seq1.fasta seq1.out

	The result in seq1.out should be the same as that in test1.disu.

Scripts in bin subdirectory:

	predict_disu.sh  input_file  ouptut_file:  (Recommended)
		predict disulfide bonds without using secondary structure

	predict_dis_ss.sh input_file output_file: 
		predict disufilde bonds using secondary structure information.
	
	Notice: In the input file, the sequence must on one single line and
                can be up to a few thousand residues.

Enjoy it!