An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes

TitleAn orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
Publication TypeJournal Article
Year of Publication2003
AuthorsKortemme, T., Morozov A. V., & Baker D.
JournalJournal of molecular biology
Volume326
Issue4
Pagination1239-59
Date Published2003 Feb 28
ISSN0022-2836
KeywordsAmino Acid Sequence, Amino Acids, Hydrogen Bonding, Mathematics, Primary Publication, Protein Conformation, Proteins
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.

Alternate JournalJ. Mol. Biol.
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