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Open Access Methodology article

Stereochemical errors and their implications for molecular dynamics simulations

Eduard Schreiner1, Leonardo G Trabuco2, Peter L Freddolino3 and Klaus Schulten4*

Author Affiliations

1 Beckman Institute for Advanced Science Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

2 CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany

3 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA

4 Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

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BMC Bioinformatics 2011, 12:190  doi:10.1186/1471-2105-12-190

Published: 23 May 2011

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.