Validating the use of database potentials in protein structure determination by NMR

FEBS Lett. 2005 Oct 24;579(25):5542-8. doi: 10.1016/j.febslet.2005.09.017. Epub 2005 Sep 27.

Abstract

The refinement of protein structures determined by nuclear magnetic resonance spectroscopy against database potentials of mean force allows for the exclusion of unfavourable conformations of the protein backbone during a structure calculation, resulting in protein structures with a marked improvement in Ramachandran statistics. In this communication, we use multiple sets of residual dipolar couplings as quality assessment criteria for several proteins and show that not only do the Ramachandran and structural quality statistics improve, but a significant improvement in the accuracy of structures is achieved upon refinement.

Publication types

  • Validation Study

MeSH terms

  • Data Interpretation, Statistical
  • Databases, Protein* / statistics & numerical data
  • Nuclear Magnetic Resonance, Biomolecular*
  • Protein Conformation*

Associated data

  • PDB/1D3Z
  • PDB/1GHH
  • PDB/1KHM
  • PDB/1VKR
  • PDB/1Z2Q