Journal
JOURNAL OF MOLECULAR BIOLOGY
Volume 326, Issue 4, Pages 1239-1259Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
DOI: 10.1016/S0022-2836(03)00021-4
Keywords
hydrogen bond; electrostatics; protein docking; protein design; free energy function
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Hydrogen bonding is a key contributor to the specificity of intramolecular and intermolecular interactions in biological systems. Here, we develop an orientation-dependent hydrogen bonding potential based on the geometric characteristics of hydrogen bonds in high-resolution protein crystal structures, and evaluate it using four tests related to the prediction and design of protein structures and protein-protein complexes. The new potential is superior to the widely used Coulomb model of hydrogen bonding in prediction of the sequences of proteins and protein-protein interfaces from their structures, and improves discrimination of correctly docked protein-protein complexes from large sets of alternative structures. (C) 2003 Elsevier Science Ltd. All rights reserved.
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