STRIKE: A Protein-Protein Interaction Classification Approach, (to appear). Software Tools and Algorithms for Biological Systems, Springer.

Strike is a program which classifies protein-protein interaction into “interacting” and “non-interacting” sets based solely on amino acid sequence information. The classification is made by applying the string kernel technique. Two proteins are classified “interacting” if they contain similar subsequences of amino acids.

The tool runs under windows platform (cygwin). A Linux based version will soon be available.
STRIKE Download
Datasets Download

Usage:
perl STRIKE.pl [input file] [ptr] [ntr] [pts] [nts] [n] [lamda]

input file: the file contains the protein interaction pairs
ptr: the number of positive training examples
ntr: the number of negative training examples
pts: the number of positive testing examples
nts: the number of negative testing examples
n: the lenght of the subsequence
lambda: the weighted decay factor

e.g: perl STRIKE.pl sample.txt 2 2 2 2 5 0.1