Assessment of protein side-chain conformation prediction methods in different residue environments.

ABSTRACT: Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic-detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at pr

SUBMITTER: Peterson LX 

PROVIDER: S-EPMC5007623 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature