title: Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.
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.
authors: Department of Computer Science, University of North Carolina, 201 South Columbia Street, Chapel Hill, North Carolina 27599, United States
authors: Matthew J
authors: MJ
authors: O'Meara
authors: Andrew
authors: A
authors: Leaver-Fay
authors: Michael D
authors: MD
authors: Tyka
authors: Amelie
authors: A
authors: Stein
authors: Kevin
authors: K
authors: Houlihan
authors: Frank
authors: F
authors: DiMaio
authors: Philip
authors: P
authors: Bradley
authors: Tanja
authors: T
authors: Kortemme
authors: David
authors: D
authors: Baker
authors: Jack
authors: J
authors: Snoeyink
authors: Brian
authors: B
authors: Kuhlman
mesh_terms: D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D012984:Software; D055672:Static Electricity