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An improved hydrogen bond potential: Impact on medium resolution protein structures
Author(s) -
Fabiola Felcy,
Bertram Richard,
Korostelev Andrei,
Chapman Michael S.
Publication year - 2002
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.4890102
Subject(s) - hydrogen bond , macromolecule , force field (fiction) , chemical physics , hydrogen , low barrier hydrogen bond , acceptor , chemistry , bond length , field (mathematics) , computational chemistry , crystallography , materials science , molecule , physics , crystal structure , mathematics , quantum mechanics , organic chemistry , biochemistry , pure mathematics
A new semi‐empirical force field has been developed to describe hydrogen‐bonding interactions with a directional component. The hydrogen bond potential supports two alternative target angles, motivated by the observation that carbonyl hydrogen bond acceptor angles have a bimodal distribution. It has been implemented as a module for a macromolecular refinement package to be combined with other force field terms in the stereochemically restrained refinement of macromolecules. The parameters for the hydrogen bond potential were optimized to best fit crystallographic data from a number of protein structures. Refinement of medium‐resolution structures with this additional restraint leads to improved structure, reducing both the free R‐factor and over‐fitting. However, the improvement is seen only when stringent hydrogen bond selection criteria are used. These findings highlight common misconceptions about hydrogen bonding in proteins, and provide explanations for why the explicit hydrogen bonding terms of some popular force field sets are often best switched off.