Abstract

Article info 2014 2 (1)    002  (01)   pp.  26 ~ 37
Title Side-chain Prediction and Computational Protein Design Problems
Authors Deok-Soo Kim¹²*, and Joonghyun Ryu2Kim²
Institutions ¹Department of Mechanical Engineering, ²Voronoi Diagram Research Center, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791, Korea. *Correspondence: dskim@hanyang.ac.kr
Abstract 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 well-known computer programs and algorithms related with computational protein design are also reviewed.