PDIviz

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Type PyMOL Plugin
Download http://melolab.org/pdiviz/
Author(s) Judemir Ribeiro
License MIT

Description

This plugin provides three distinct coloring modes to highlight interactions with DNA bases and backbone, major and minor groove, and with atoms of different pharmacophoric type (hydrogen bond donors/acceptors, hydrophobic and thymine methyl). Each mode comes in three styles to focus the visual analysis on the protein or DNA side of the interface, or on the nucleotide sequence.

PDIviz also allows for the generation of publication quality images, all calculated data can be written to disk, and a command line interface is provided for automating tasks. The plugin may be helpful for the detailed identification of regions involved in DNA base and shape readout, and can be particularly useful in rapidly pinpointing the overall mode of interaction.

Interactions are calculated using the solvent accessible surface area (SASA), so we validated the Get_Area function against NACCESS using a non-redundant set of protein-DNA complexes, obtaining a RMSD of just 0.078 Ų, after correcting the van der Waals radii for all heavy atoms.

Installation

Simply download the plugin and install using PyMOL's plugin manager. Compatible with Linux, OSX and Windows.

Visualizations

PDIviz has three main visualization modes focusing on the interactions on the dna backbone and bases, major and minor groove, and pharmacophoric interactions (h-bond donors/acceptors).