Enzyme Redesign by SVM

In [1], a new support vector machine (SVM)-based approach was proposed to predict the substrate (adenylation domain, or A domain in short) specificity of subtypes of a given protein sequence family (nonribosomal peptide synthetases, or NRPS in short). Based on the physico-chemical properties of the amino acids, the residues of NRPS were first encoded into vectors in high dimensional feature space. A dataset of A domains with known specificities compiled from the literature is used to train the SVM classifier, based on which we can predict the specificity of a new A domain. The machine learning approach can be generalized to the prediction of functional subspecificities of other classes of enzymes that “share a conserved structure but catalyze different substrates”.