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State-of-the-art, structure-based method for assessing the energetics of water-solvating ligand binding sites for ligand optimization

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Discover new possibilities for ligand design

WaterMap is an advanced solution for the reliable calculation of positions and energies of solvating water in a protein binding pocket. By providing key insights to guide ligand design and optimization, WaterMap is a high impact solution for structure-based drug discovery, as demonstrated in several successful drug discovery programs now in clinical development.

Key Capabilities

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Predict the location and thermodynamic potential of high-energy, displaceable water molecules in the binding site to guide drug design
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Gain insights into the pocket properties and hydrophobic forces driving the binding of small molecules
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Visualize hydration sites for an easy method of interpreting SAR and gain insights to improve potency and selectivity
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Apply WaterMap to a wide range of systems including enzymes, GPCRs, bromodomains, nucleic acids, and protein-protein interfaces
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Case StudyDiscovery of a novel, potent ACC inhibitor using WaterMap

Computationally-guided design and assessment of water energetics in the binding site

Discovery of a novel, potent ACC inhibitor using WaterMap

See how Nimbus Therapeutics identified potent, selective inhibitors using a virtual screening workflow guided by hydration energetics.

read the case study


Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

Life Science
Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity
Life Science
Decisive role of water and protein dynamics in residence time of p38′ MAP kinase inhibitors
Life Science
Potency-Enhancing Mutations of Gating Modifier Toxins for the Voltage-Gated Sodium Channel NaV1.7 Can Be Predicted Using Accurate Free-Energy Calculations
Life Science
Water Thermodynamics of Peptide Toxin Binding Sites on Ion Channels
Life Science
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Life Science
The Role of Bridging Water and Hydrogen Bonding as Key Determinants of Noncovalent Protein-Carbohydrate Recognition
Life Science
Shedding Light on Important Waters for Drug Design: Simulations versus Grid-Based Methods
Life Science
Calculating Water Thermodynamics in the Binding Site of Proteins – Applications of WaterMap to Drug Discovery
Life Science
Accelerating Drug Discovery Through Tight Integration of Expert Molecular Design and Predictive Scoring
Life Science
Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation
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Training & Resources

Online certification courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.


Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.