PDIviz: analysis and visualization of protein-DNA binding interfaces.

Judemir Ribeiro,Andreas Schüller,Francisco Melo

doi:10.1093/bioinformatics/btv203

Judemir Ribeiro, Andreas Schüller + Show 1 more

Open Access

https://doi.org/10.1093/bioinformatics/btv203

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Abstract

Summary: Specific recognition of DNA by proteins is a crucial step of many biological processes. PDIviz is a plugin for the PyMOL molecular visualization system that analyzes protein–DNA binding interfaces by comparing the solvent accessible surface area of the complex against the free protein and free DNA. The plugin provides three distinct three-dimensional visualization 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 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.Availability and implementation: Freely available at http://melolab.org/pdiviz/ as a PyMOL plugin. Tested with incentive, educational, and open source versions of PyMOL on Windows, Mac and Linux systems.Contact: aschueller@bio.puc.clSupplementary Information: Supplementary data are available at Bioinformatics online.

Highlights

Specific recognition of DNA by proteins is a prerequisite of many biological processes and is essentially understood when analyzed at a three-dimensional (3D) structural level
Protein–DNA interactions are complex and a simple recognition code does likely not exist (Slattery et al, 2014). 3D visual analysis of protein–DNA complexes today often requires the use of several computer programs for contact analysis and visualization
Protein–DNA interface detection is based on the method of differential solvent accessible surface area estimation

Summary

Introduction

Specific recognition of DNA by proteins is a prerequisite of many biological processes and is essentially understood when analyzed at a three-dimensional (3D) structural level. We present PDIviz, a plugin for the PyMOL molecular visualization system (Schrodinger, LLC) that is designed to visualize protein–DNA interfaces and to focus visual analysis on various aspects of protein–DNA interactions. Protein–DNA interface detection is based on the method of differential solvent accessible surface area estimation.

Results

Conclusion