Abstract
BackgroundNormal 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.ResultsΔΔPT 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.ConclusionsThis 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.
Highlights
Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules
Normal mode calculation is based on the harmonic approximation of the potential energy function, V, around a minimum energy conformation, Equation 1, where r is the distance between atoms, R is the equilibrium distance between atoms, u is the difference from equilibrium distance between atoms, i and j refer to the atom number, and α and β refer to the direction of the motion
Normal mode analysis (NMA) is a powerful tool for the study of protein movements, conformational changes, and protein entropy
Summary
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 allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies
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