Journal article

Refinement of protein structures in explicit solvent

Linge J, Williams M, Spronk C, Bonvin A, Nilges M ...see all

Proteins: Structure, Function and Genetics, vol. 50, issue 3 (2003) pp. 496-506

  • 108


    Mendeley users who have this article in their library.
  • 458


    Citations of this article.
  • N/A


    ScienceDirect users who have downloaded this article.
Sign in to save reference


We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g., homology modeling or threading) or experimental methods (e.g., NMR). In contrast to other recently proposed refinement protocols, we put a strong emphasis on consistency with widely accepted covalent parameters and computational efficiency. We illustrate the method for NMR structure calculations of three proteins: interleukin-4, ubiquitin, and crambin. We show a comparison of their structure ensembles before and after refinement in water with and without a force field energy term for the dihedral angles; crambin was also refined in DMSO. Our results demonstrate the significant improvement of structure quality by a short refinement in a thin layer of solvent. Further, they show that a dihedral angle energy term in the force field is beneficial for structure calculation and refinement. We discuss the optimal weight for the energy constant for the backbone angle omega and include an extensive discussion of meaning and relevance of the calculated validation criteria, in particular root mean square Z scores for covalent parameters such as bond lengths.

Author-supplied keywords

  • Dihedral angle
  • Force field
  • Molecular dynamics
  • NMR
  • Omega angle
  • Protein structure
  • Validation
  • Water refinement

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Get full text


Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free