Learning to discriminate between ligand-bound and disulfide-bound cysteines

We present a machine learning method to discriminate between cysteines involved in ligand binding and cysteines forming disulfide bridges. Our method uses a window of multiple alignment profiles to represent each instance and support vector machines with a polynomial kernel as the learning algorithm. We also report results obtained with two new kernel functions based on similarity matrices. Experimental results indicate that binding type can be predicted at significantly higher accuracy than using PROSITE patterns.