A spectrum of phylogenetic-based approaches for predicting protein functional sites

Abstract

This chapter introduces four distinct, yet aligned, computational approaches to predict protein functional sites. The methods range from simple alignment conservation scores to more sophisticated phylogenetic-based approaches (i.e., evolutionary trace, ConSurf, and phylogenetic motifs). Each approach and its theoretical underpinnings are discussed in detail. Key differences within later revisions of each method (when appropriate) are also provided. Applications of the method and how it has been assessed are also discussed for several methods. Finally, information on availability of each method is provided.