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??PT: a comprehensive toolbox for the analysis of protein motion.

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:??PT 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.

SUBMITTER: Rodgers TL

PROVIDER: S-EPMC3689072 | biostudies-literature | 2013 Jun

REPOSITORIES: biostudies-literature

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ΔΔPT: a comprehensive toolbox for the analysis of protein motion.

Rodgers Thomas L TL Burnell David D Townsend Phil D PD Pohl Ehmke E Cann Martin J MJ Wilson Mark R MR McLeish Tom C B TC

BMC bioinformatics 20130607

<h4>Background</h4>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.<h4>Results</h4>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. ...[more]

PMID: 23758746

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