Construction of a Sequence- and Backbone-Dependent Rotamer Library by Hidden-Markov Model

Abstract

Sidechain prediction is an important subproblem of protein design and structure prediction. Construction of rotamer library is the basis for protein sidechain prediction because it provides the basic searching space for prediction. However, the state-of-the-art rotamer libraries focus on the statistical information of individual amino acids, ignoring the direct affection of its adjacent amino acids. This article presents a sequence- and backbone-dependent rotamer library. Both the conformation information of adjacent amino acids and torsion angle of the current residue are taken into account to construct a sequence- and backbone-dependent library by HMM. Evaluation on all 13 free modeling targets of CASP8 based on our rotamer library is conducted. Comparing with side-chain prediction based on the state-of-the-art rotamer library, our library outperforms the sidechain prediction accuracy on all the test targets to a certain extent.