Side-chain Prediction and Computational Protein Design Problems

Abstract

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