The FunFOLD Ligand Binding Residue Prediction Method
----------------------------------------------------

Version 1.01 (May 2011)

(c) Liam J. McGuffin, Stuart J. Tetchner, Daniel B. Roche

Description
-----------

A method for predicting the ligand binding site residues in a protein using a 3D model and a list of templates.

References
----------

Roche, D. B., Tetchner, S. J. & McGuffin, L. J. (2011) FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics, In press.

Installation
------------

No installation is required for the FunFOLD program itself after you have downloaded the file. The program is provided in the form of an executable jar file (FunFOLD.jar). The instructions below are for Linux (bash) but equivalent commands can be used in other Unix based OSes.

Requirements:

1. A recent version of Java (java.com/getjava/).
2. A recent version of PyMOL (www.pymol.org).
3. The TMalign program (http://zhanglab.ccmb.med.umich.edu/TM-align/). Please ensure the TMalign program is working on your system before attempting to run FunFOLD. Ensure that you have the correct 32bit/64bit version for your hardware and that the TMalign file is made executable:
chmod +x TMalign

4. wget installed system wide.

Running the program
-------------------

You can simply edit the shell script (FunFOLD.sh) or you can follow the steps below.

1. (optional) Set the bash environment variable for Java, if you have not installed it system wide, TMalign and PyMOL. e.g.

export JAVA_HOME=/home/Liam/jdk1.6.0/
export TMALIGN_HOME=/home/Liam/programs/bin/
export PYMOL_HOME=/usr/bin/

2. Run FunFOLD. For example, if your path to the model was /home/Liam/FunFOLD/T0470/MUProt_TS3, your list of templates was /home/Liam/FunFOLD/T0470/T0470_PARENT.dat, your target was called T0470 and your output directory was /home/Liam/FunFOLD/T0470/:

$JAVA_HOME/bin/java -jar FunFOLD.jar /home/Liam/FunFOLD/T0470/MUProt_TS3 /home/Liam/FunFOLD/T0470/T0470_PARENT.dat T0470 /home/Liam/FunFOLD/T0470/

Or, if you have java installed system wide:

java -jar FunFOLD.jar /home/Liam/FunFOLD/T0470/MUProt_TS3 /home/Liam/FunFOLD/T0470/T0470_PARENT.dat T0470 /home/Liam/FunFOLD/T0470/

Or, using the shell script provided:

./FunFOLD.sh /home/Liam/FunFOLD/T0470/MUProt_TS3 /home/Liam/FunFOLD/T0470/T0470_PARENT.dat T0470 /home/Liam/FunFOLD/T0470/

IMPORTANT: Please also note that you should use FULL PATHS for your input files and output directory, the output directory should also end with a "/" and must contain the input model.

Output
------

An example of output for target T0470 can be found in the file T0470.tar.gz. The important example files containing information about the prediction are:

T0470_FN.txt - the final prediction in CASP FN format
T0470_lig.pdb - PDB file containing a superposition of all ligands and templates with the model
T0470_lig2.pdb - PDB file of the model with all possible ligands
T0470_binding_site.png - an auto generated image of the binding site
pymol.script - pymol script used to generate the image


Trouble Shooting
----------------

Email me: l.j.mcguffin@reading.ac.uk

I will try to respond to your issue as soon as I can!

Thanks,
Liam