GIST-gpu

GIST-gpu computes solvation free energies and maps thermodynamic properties of water around proteins using grid inhomogeneous solvation theory (GIST) to assess local hydrophobicity.

Key Features:

• GPU Acceleration: Uses GPU acceleration to reduce computation time for GIST calculations on large biomolecular systems.
• Solvation Free Energy Calculation: Calculates solvation free energy by quantifying thermodynamic properties of water molecules in proximity to protein structures.
• Hydrophobicity Evaluation: Evaluates localized protein surface hydrophobicity by mapping solvation free energies onto spatial grids around biomolecular interfaces.

Scientific Applications:

• Protein Binding Studies: Analyzes hydrophobicity of binding interfaces and correlates interface hydrophobicity with bound peptide hydrophobicity, demonstrated on nine proteases.
• Structure-Based Drug Design: Provides detailed thermodynamic profiles of protein–water interactions to inform structure-based drug design.

Methodology:

Implements grid inhomogeneous solvation theory (GIST) to map thermodynamic properties of water onto a spatial grid and compute solvation free energy around proteins, with computations accelerated on GPUs.