Schrodinger WaterMap-v38011

Schrodinger WaterMap v38011 is a computational chemistry tool for mapping and quantifying the thermodynamics of water molecules in and around protein binding sites. By running short explicit-solvent simulations and applying inhomogeneous solvation theory, it identifies hydration sites and estimates their enthalpic, entropic, and free-energy contributions. These insights help medicinal chemists pinpoint displaceable waters, reveal ligandable hotspots, and rationalize structure–activity relationships to guide lead optimization.

Key capabilities:

• Locates and clusters hydration sites in protein pockets from molecular dynamics trajectories.
• Computes per-site thermodynamics (enthalpy, entropy, free energy) to rank displaceable waters.
• Highlights hotspots to support ligand design decisions such as adding, removing, or repositioning functional groups.
• Integrates with common structure-based workflows for docking and binding-site analysis; produces maps and tabular summaries for visualization and reporting.
• Supports typical protein/ligand structure inputs and generates interpretable, publication-ready figures and data tables.

Typical use cases:

• Prioritizing waters to target or retain in structure-based design.
• Explaining potency shifts and SAR across congeneric series.
• Discovering cryptic or transient pockets and opportunities for ligand growth.

Notes:

• Build: v38011. Feature set and platform support may depend on your licensed Schrödinger environment. Consult your organization’s license and documentation for exact compatibility and usage details.

Schrodinger WaterMap-v38011 is developed by Schrodinger LLC. The most popular version of this product among our users is 3.8.