The Binding-site Distance Test scoring method
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Version 1.0 (Aug 2010)

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

Description
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A method for scoring the accuracy of protein binding site predictions.

References
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Roche, D. B., Tetchner, S. J. & McGuffin, L. J. (2010) The Binding Site Distance Test Score: A robust method for the assessment of predicted protein binding sites. Bioinformatics, In press.

Installation
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No installation is required for the BDT program itself after you have downloaded the file. The program is provided in the form of an executable jar file (BDT.jar) and should run on most operating systems where Java is installed. The instructions below are for Linux (bash) but equivalent commands can be used in other OSes.

Requirements:

1. A recent version of Java (java.com/getjava/).


Running the program
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You can simply edit the shell script (BDT.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. e.g.

export JAVA_HOME=/home/Liam/jdk1.6.0/

2. Run BDT. For example, if the predicted residues in the protein are "75,79,82,84", the observed residues are "76,77,78,83", the PDB file of the target is /home/Liam/data/CASP8_server_models/T0453/T0453.CA and the distance treshold is 3.0 Angstroms:

$JAVA_HOME/bin/java -jar BDT.jar 75,79,82,84 76,77,78,83 /home/Liam/data/CASP8_server_models/T0453/T0453.CA 3.0

Or, if you have java installed system wide:

java -jar BDT.jar 75,79,82,84 76,77,78,83 /home/Liam/data/CASP8_server_models/T0453/T0453.CA 3.0

Or, using the shell script provided:

./BDT.sh 75,79,82,84 76,77,78,83 /home/Liam/data/CASP8_server_models/T0453/T0453.CA 3.0

Output
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The program outputs both the Matthews Correlation Coefficient (MCC) and the Binding-site Distance Test (BDT) score for comparison. 

Output from the above example using the file T0453.CA is shown below:

TP=0 FP=4 TN=79 FN=4
Matthews Correlation Coefficient (MCC) = -0.04819277108433735
Sum of maxSi = 1.5351355650814271
Normalisation = 4.0
Binding-site Distance Test (BDT) score = 0.3837838912703568


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

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

Thanks,
Liam