Ligand-binding Residue Prediction

In this chapter, we explore means for predicting protein residues that interact with small molecules. We will motivate the problem by describing potential uses for such information and proceed to discuss methods advanced for prediction. We describe our sequence-based approach and contrast it with another current methodwhich relies on predicted protein structure to help identify ligand-binding residues. In the last part of the chapter, we employ sequence-based predictions in a homology modeling task which shows that the predictions are presently accurate enough to improve downstream performance.