****************************** README *****************************************
*  This README file has been provided to assist the user the perform          *
*  protein-protein interface residue prediction using the machine-learning    *
*  based algorithm BSpred. BSpred only uses sequence information of one       *
*  and identifies potential residues which may participate in protein-protein *
*  interaction. All questions need to addressed to the emails:                *
*  zhanglab@zhanggroup.org or srayanta@umich.edu                               *
*******************************************************************************

The directory "INSTALL_BSpred" contains the following subdirectories:
1) library : The library folder contains a non-redundant sequence database,
             NCBI BLAST programs[1] and databases, PSIPRED secondary structure
             prediction programs[2] and programs to perform solvent accessibility
             prediction[3]. Please do no make any changes to this folder.
2) bin     : The bin directory contains all programs and executables necessary 
             to run BSpred. This includes the main program "runBSpred.pl".

USAGE:

Input file: Please create a folder containing a single input file named "seq.txt"
            containing your input sequence. This is your data directory.
Run       : From your data directory please enter
            path_to_INSTALL_BSpred_directory/runBSpred.pl your_data_directory

EXPLANATIONS:

runBSpred.pl: This is the main BSpred program which needs to run by the user.

path_to_INSTALL_BSpred_directory: The full path to where the 
            INSTALL_BSpred directory has been saved on the users computer.

your_data_directory: The complete path to your data directory

EXAMPLE:

For the users convenience an example has been kept in the
INSTALL_BSpred/bin/example directory, containing a sample input sequence
file "seq.txt" and a sample output file "prediction.txt" .

Let us suppose that user X wants to BSpred on the input sequence in the "example" directory.

Step 1: User X saves the INSTALL_BSpred directory at "/home/X/INSTALL_BSpred"
Step 2: X moves to his data directory `cd /home/X/INSTALL_BSpred/bin/example`
Step 4: X runs BSpred using the following command:
        `/home/X/INSTALL_BSpred/runBSpred.pl /home/X/INSTALL_BSpred/bin/example`;

OUTPUT:

The BSpred algorithm returns the following output files to your data directory
1) prediction.txt : This is the final output generated by BSpred containing predicted interface residues.
                    Column 1- Residue Number
                    Column 2- Residue Type
                    Column 3- Confidence Score. The higher the confidence the better.
 
CITATION:

Mukherjee, Srayanta, and Yang Zhang. "Protein-protein complex structure
predictions by multimeric threading and template recombination." 
Structure 19.7 (2011): 955-966.

REFERENCES:
1) Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402.
2) Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
3) MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. (Translated from eng) Proteins 72(2):547-556 (in eng).