****************************** 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: * * yangzhanglab@umich.edu 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).