PDIviz

PDIviz identifies protein–DNA binding interfaces by calculating buried surface area and visualizing detailed protein–DNA interactions in PyMOL to support analysis of DNA base and shape readout.

Key Features:

• Interface Detection: Calculates buried surface area directly within PyMOL to identify protein–DNA binding interfaces.
• Solvent Accessible Surface Area Analysis: Compares solvent accessible surface areas (SASA) of the complex against free protein and free DNA to reveal changes upon binding.
• Three-Dimensional Visualization Modes: Displays three-dimensional representations of protein–DNA interfaces within PyMOL.
• DNA Base and Backbone Interactions: Visualizes interactions with specific DNA bases and backbone components.
• Major and Minor Groove Analysis: Highlights protein interactions with the major and minor grooves of the DNA helix.
• Pharmacophoric Atom Interactions: Maps hydrogen bond donors and acceptors, hydrophobic interactions, and thymine methyl group contacts.
• Visualization Styles: Emphasizes either the protein or DNA side of the interface and provides a nucleotide sequence–focused view.

Scientific Applications:

• DNA base and shape readout mapping: Identifies regions involved in DNA base and shape readout by proteins.
• Interaction mode determination: Determines the overall mode of interaction between proteins and DNA.
• Gene regulation and transcription factor studies: Supports analysis of transcription factor–DNA binding and gene regulation mechanisms.
• Drug design targeting protein–DNA complexes: Assists in characterizing protein–DNA interfaces relevant to drug design.

Methodology:

Leverages PyMOL to perform detailed visual analyses and generate publication-quality images, exports calculated data for further analysis, and provides a command-line interface for automation.