MolSurfer

MolSurfer integrates two-dimensional interface maps with three-dimensional structural views to visualize and analyze macromolecular interfaces and characterize physicochemical properties such as electrostatic potential and hydrophobicity.

Key Features:

• Coupled 2D/3D Visualization: Links detailed 2D projections of macromolecular interfaces to corresponding 3D structures for correlated spatial and physicochemical inspection.
• Interface Analysis with ADS: Generates analytically defined 2D interface maps using ADS software to represent interface features.
• Java PDB Viewing (WebMol): Integrates 2D maps with 3D macromolecular structures displayed via the Java PDB viewer WebMol.
• Poisson-Boltzmann Electrostatics: Computes Poisson-Boltzmann electrostatic potentials for macromolecules and maps these potentials onto interfaces.
• Physicochemical Property Mapping: Represents interface properties such as electrostatic potential and hydrophobicity on the derived maps and 3D views.

Scientific Applications:

• Protein–protein interface analysis: Applied to a set of 39 protein–protein complexes from the Protein Data Bank (PDB) to analyze interface properties.
• Protein–nucleic acid interface analysis: Supports visualization and analysis of an expanded dataset including 75 interfaces from protein–DNA and protein–RNA complexes.

Methodology:

MolSurfer generates analytically defined 2D interface maps with ADS software, integrates them with 3D structures displayed via the Java PDB viewer WebMol, and computes Poisson-Boltzmann electrostatic potentials mapped onto interfaces.