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

Authors

Lenna X Peterson, Xuejiao Kang, Daisuke Kihara

Published in

Proteins. Volume 82. Issue 9. Pages 1971-84. Epub Mar 31, 2014.

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 protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers.

PMID:
24619909
Bibliographic data and abstract were imported from PubMed on 07 Nov 2025.

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