gridSolvate

gridSolvate predicts the distribution of hydration sites and the associated excess chemical potentials of water molecules in proteins and protein–ligand complexes to characterize biomolecular hydration.

Key Features:

• Hydration Site Prediction: Identifies positions of water molecules in buried regions and within the first hydration shell of biomolecules.
• Excess Chemical Potential Calculation: Calculates the excess chemical potential (affinity) of water molecules at predicted hydration sites.
• Semiexplicit Hydration Model: Employs a semiexplicit hydration model that captures specific water–solute interactions while offering computational efficiency.
• Atomistic PDB-like Input: Uses atomistic protein structures provided in PDB-like file format as input data.

Scientific Applications:

• Protein–Ligand Interfaces: Predicts distribution and affinity of water molecules within protein–ligand interfaces to inform molecular interaction analyses relevant to drug design and biochemical research.
• Validation and Accuracy: Demonstrated validated performance by correctly identifying 77% of interface water molecules in an external test set.

Methodology:

Merges previous research on bulk hydration of drug-like solutes with determination of protein hydration sites using a semiexplicit hydration model that was previously introduced and validated.