Stereochemical errors and their implications for molecular dynamics simulations

BMC Bioinformatics. 2011 May 23;12:190. doi: 10.1186/1471-2105-12-190.


Background: Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.

Results: Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.

Conclusions: Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acids / chemistry
  • Models, Molecular
  • Molecular Dynamics Simulation*
  • Nucleic Acids / chemistry
  • Nucleosides / chemistry
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Software*


  • Amino Acids
  • Nucleic Acids
  • Nucleosides
  • Proteins