DelPhiForce

DelPhiForce computes and visualizes long-range electrostatic forces and electrostatic potentials for irregularly shaped biomolecules in aqueous environments at user-defined positions.

Key Features:

• DelPhi integration: Implements and extends the DelPhi electrostatic framework for force and potential calculations.
• Electrostatic force and potential calculation: Computes long-range electrostatic forces and electrostatic potentials at user-defined positions in biomolecular systems.
• Interpolation methods: Implements triquadratic and tricubic interpolation methods to model electrostatic potential with high spatial accuracy.
• Validation at high resolution: Tricubic interpolation was validated against analytical solutions showing negligibly small errors at 4 grids per angstrom (Å).
• Irregular shapes and aqueous environments: Handles electrostatics for irregularly shaped molecules immersed in aqueous environments.
• Visualization output: Produces outputs compatible with VMD (Visual Molecular Dynamics) for visualization of electrostatic forces.
• Application to protein–protein complexes: Has been applied to three protein–protein complexes to reveal electrostatic guidance toward native interfaces and electrostatic torque for non-native orientations.

Scientific Applications:

• Protein–protein interaction analysis: Quantifies forces between binding partners to assess electrostatic guidance and torque during complex formation.
• Macromolecular electrostatics: Studies long-range electrostatic interactions in biomolecules including proteins, DNAs, lipids, and small molecules.
• Molecular recognition and orientation: Evaluates how electrostatic potentials influence molecular recognition, binding orientation, and approach trajectories.

Methodology:

Built on the DelPhi algorithm and employing triquadratic and tricubic interpolation to compute electrostatic potentials and forces at user-defined positions, with tricubic interpolation validated against analytical solutions at 4 grids per Å.