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ProDy

Generates structures by performing molecular normal mode analysis of input structure using the open-source molecular dynamics package ProDy.

Accessibility

The ProDy module is accessible from the Simulate section of the main menu.

Basic Usage

The purpose of the module is perform generate normal mode trajectories of an input protein structure.

Notes

Screen Shots and Description of Input Fields

This example generates a set of 5 normal modes using the ProDy ANM module for the lysozyme protein.

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Example Output

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Results are written to a new directory within the given "run name" as noted in the output.

Several files are generated and saved to the "run name" prody directory: the output DCD file containing merged trajectories for modes 1 to 5; separate DCD files for individual trajectories along each mode; a DCD and PDB file with an ensemble of randomly-sampled conformations from each of the normal modes; a file containing the Kirchhoff matrix; a file containing the hessian matrix; a file with ANM results in NMD format for subsequent visualization; two additional files with ANM results in NMD format with normal modes extended to back-bone and all atoms, respectively; two text files with eigenvalues and eigenvectors, respectively; a text file containing square fluctuations along each mode; a text file with cross-correlations; a text file with the covariance matrix constructed using the 5 modes; and a text file with the β-value (temperature factor) of the course-grain atom on each residue.

Visualization

The first image below shows an animation of the first (lowest frequency) normal mode. The image was generated by uploadng the file with normal modes extended to all atoms using the VMD Normal Mode Wizard. A short step-by-step guide to creating this image can be found on the VMD visualization/animation of normal modes page. A more detailed tutorial on the use of VMD's Normal Mode Wizard can be found on the ProDy_NMWiz tutorial site.

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The three residues highlighted in yellow emphasize stretching of bonds to lengths that are not physically realistic.
The image below shows the analogous animation after the original trajectory for the first mode is subjected to 1000 steps of Energy Minimization.

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This is further demonstrated in the third image below, which shows a plot of the root mean square deviation (RMSD), relative to input structure, versus frame number (for residue 118-the middle residue of the highlighted three) for the trajectory along the first mode from ProDy, before and after Energy Minimization.

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This, shows that energy minimization can remove the physically unrealistic bond stretches, restoring those structures that deviate far from the initial input structure.

Energy Minimization Input Fields

Below is an example of the inputs needed to perform a 1000 step Energy Minimization of the trajectory for the first normal mode, traverse_0.dcd.

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Example Output

Upon completion, the output screen should look something like the one below.

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Visualization

The trajectories for traverse0.dcd and mintraverse_0.dcd can be directly compared in VMD to see the effect of the 1000 step minimization.

Files Used and Created in Example

Advanced Input Options (NOT YET IMPLEMENTED!)

Advanced options are not yet implemented. ProDy will not run if the Check Box for Advanced Input is checked.

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The input variables are listed below.

Reference(s) and Citations

  1. ProDy: Protein Dynamics Inferred from Theory and Experiments A. Bakan, L.M. Meireles, I. Bahar, Bioinformatics 27, 1575-1577 (2011). BIBTeX, EndNote, Plain Text

  2. Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor P. Doruker, A. R. Atilgan, I. Bahar, Proteins 40, 512-524 (2000). BIBTeX, EndNote, Plain Text

  3. Anisotropy of fluctuation dynamics of proteins with an elastic network model A. R. Atilgan, S. R. Durrell, R. L. Jernigan, M. C. Demirel, O. Keskin, I. Bahar I. Biophys. J. 80, 505-515 (2001) BIBTex, Endnote, Plain Text

  4. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text

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