doi: 10.1016/s0022-2836(03)00021-4.
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
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- PMID: 12589766
- DOI: 10.1016/s0022-2836(03)00021-4
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An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
J Mol Biol.
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Abstract
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.
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