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J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

Author information

1
Department of Computer Science, University of North Carolina, 201 South Columbia Street, Chapel Hill, North Carolina 27599, United States

Abstract

Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics. The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal structures. The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations and establishes a new standard energy function for Rosetta.

PMID:
25866491
PMCID:
PMC4390092
DOI:
10.1021/ct500864r
[Indexed for MEDLINE]
Free PMC Article

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