title: Stereochemical errors and their implications for molecular dynamics simulations.
abstract: 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.
authors: Beckman Institute for Advanced Science Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors: Eduard
authors: E
authors: Schreiner
authors: Leonardo G
authors: LG
authors: Trabuco
authors: Peter L
authors: PL
authors: Freddolino
authors: Klaus
authors: K
authors: Schulten
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