Side-chain Prediction and Computational Protein Design Problems

Protein is fundamental for life and thus protein design has been one of the hottest research issues since a couple of decades ago and computational approach has been developed with some significant design cases with experimental verification. One of the fundamental building blocks of computational protein design is to predict side-chain conformation of backbone structure. This paper first reviews prior efforts of computationally predicting sidechains of a given backbone and then reviews computational protein design efforts based on side-chain prediction. The paper views computational protein design problem as three categories: Redesign, De novo design of Type I, and De novo design of Type II. Some wellknown computer programs and algorithms related with computational protein design are also reviewed.