A three-dimensional potential of mean force to improve backbone and sidechain hydrogen bond geometry in Xplor-NIH protein structure determination

Protein Sci. 2020 Jan;29(1):100-110. doi: 10.1002/pro.3745. Epub 2019 Oct 27.


We introduce a new hydrogen bonding potential of mean force generated from high-quality crystal structures for use in Xplor-NIH structure calculations. This term applies to hydrogen bonds involving both backbone and sidechain atoms. When used in structure refinement calculations of 10 example protein systems with experimental distance, dihedral and residual dipolar coupling restraints, we demonstrate that the new term has superior performance to the previously developed hydrogen bonding potential of mean force used in Xplor-NIH.

Keywords: hydrogen bond; potential of mean force; protein; structure determination.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Computational Biology / methods*
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Protein Conformation
  • Proteins / chemistry*
  • Software


  • Proteins