MPlot

MPlot analyzes and visualizes tertiary-structure contacts and geometrical features of helical membrane proteins.

Key Features:

• Input Requirements: Accepts experimentally determined or computationally modeled protein structures in PDB format.
• Van der Waals and Geometric Measures: Calculates cut-off dependent van der Waals contacts and crossing angles between transmembrane helices.
• Hydrogen Bonds and Membrane Planes: Computes main-chain and side-chain hydrogen bonds and determines membrane planes using integrated third-party tools.
• Extensibility: Supports construction of new workflows by combining existing tools or substituting intermediate results with external outputs.
• Visualization Outputs: Produces Jmol-compatible visualizations and automatically generated PyMOL scripts for structural inspection.
• Graphical and Data Export: Generates 2D graphs showing spatial arrangement of transmembrane helices at true-to-scale distances and exports all analysis results as text files.

Scientific Applications:

• Helix–Helix Interaction Analysis: Characterizes helix–helix contacts and crossing geometries in helical membrane proteins.
• Membrane Embedding and Geometry Studies: Assesses membrane plane positioning and spatial arrangement of transmembrane helices.
• Validation of Structure Predictions: Provides text outputs suitable for statistical evaluation and validation of knowledge-based tertiary structure prediction tools.

Methodology:

Integrates in-house and third-party computational tools to calculate cut-off dependent van der Waals contacts, crossing angles between transmembrane helices, main-chain and side-chain hydrogen bonds, membrane planes, and to generate PyMOL scripts and text-file exports.