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Open Access Highly Accessed Software

Δ ΔPT: a comprehensive toolbox for the analysis of protein motion

Thomas L Rodgers12*, David Burnell12, Phil D Townsend13, Ehmke Pohl123, Martin J Cann13, Mark R Wilson12 and Tom CB McLeish14

Author Affiliations

1 Biophysical Sciences Institute, Durham University, Durham, UK

2 Department of Chemistry, Durham University, Durham, UK

3 School of Biological and Biomedical Sciences, Durham University, Durham, UK

4 Department of Physics, Durham University, Durham, UK

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BMC Bioinformatics 2013, 14:183  doi:10.1186/1471-2105-14-183

Published: 7 June 2013

Abstract

Background

Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies.

Results

ΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies.

Conclusions

This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software.