Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library.

ABSTRACT: Accurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side-chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small-molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first-principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only

SUBMITTER: Peterson RW 

PROVIDER: S-EPMC2286725 | biostudies-literature | 2004 Mar

REPOSITORIES: biostudies-literature