DDPT: a comprehensive toolbox for the analysis of protein motion

Rodgers Thomas, L; Burnell, David; Townsend, Phil D; Pohl, Ehmke; Cann, Martin J; Wilson, Mark R; McLeish, Tom CB

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.

Citation

Rodgers Thomas, L., Burnell, D., Townsend, P. D., Pohl, E., Cann, M. J., Wilson, M. R., & McLeish, T. C. (2013). DDPT: a comprehensive toolbox for the analysis of protein motion. BMC Bioinformatics, 14(1), Article 183. https://doi.org/10.1186/1471-2105-14-183

• Journal Article Type: Article
• Publication Date: Jun 1, 2013
• Deposit Date: Jun 21, 2013
• Publicly Available Date: Aug 21, 2013
• Journal: BMC Bioinformatics
• Electronic ISSN: 1471-2105
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 1
• Article Number: 183
• DOI: https://doi.org/10.1186/1471-2105-14-183
• Public URL: https://durham-repository.worktribe.com/output/1481494