A recent publication at BMC Bioinformatics describes two VMD plugins that can be used to detect, visualize, and correct stereochemical errors in macromolecular structures. The plugins can also be used to generate restraints that prevent chirality and peptide bond configuration errors from arising in simulations where high forces are applied, such as MDFF simulations. Use of the plugins is described in the Structure Check Tutorial.
Stereochemical errors and their implications for molecular dynamics simulations.
Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, and Klaus Schulten. BMC Bioinformatics, 12, 190, 2011.
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.