PredDimer is an algorithm to predict heterodimeric protein complexes with pairwise kernel function and Support Vector Machines (SVM). Please read paper Improving prediction of heterodimeric protein complexes using combination with pairwise kernel for details.
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
What things you need to install the software and how to install them
- Library: libsvm-3.0.2
- Programming language: C++
- cyc2008.data - downloaded from cyc2008
- pro200600448_3_s.csv - downloaded from WI-PHI
- uniprot_sprot_fungi.dat - downloaded from UniProtKB
g++ pairwise-kernel.cpp -o dimer
./dimer 1 2 3 4 5 8 9 a filename1.txt filename2.txt
./svm-train -q -t 4 -v 10 -w1 b -w-1 c filename2.txt
a: b: weight of positive examples c: weight of negative examples