Fast, accurate, and intuitive binding site identification

Industry-leading platform to discover and optimize better molecules, faster

Understand protein binding sites to enhance drug design

Identifying druggable pockets is an important early challenge in a structure-based first-in-class drug discovery project. However, locating these sites in drug design projects is often challenging. SiteMap’s proven algorithm helps identify binding sites, including allosteric binding sites and protein-protein interfaces, and evaluate their druggability. In addition to impacting lead discovery, SiteMap can assist researchers in lead optimization by providing insights into potential ligand-receptor interactions which can then guide modification of lead compounds to increase their binding potency.

Key Capabilities

Rapidly identify and rank binding sites
Rapidly identify and rank binding sites

Locate binding sites whose size, functionality, and extent of solvent exposure meet user specifications. Rank possible binding sites using physics-based criteria tuned to eliminate those not likely to be pharmaceutically relevant using SiteScore, the scoring function used to assess a site’s propensity for ligand binding.

Easy-to-use graphical interface
Easily visualize binding sites

Easily visualize binding sitesIdentify regions within the binding site suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors, acceptors, or metal-binding functionality. Distinguish different binding site sub-regions which allows for ready assessment of a ligand’s complementarity.

Seamlessly proceed to docking and virtual screens on identified sites
Seamlessly proceed to docking and virtual screens on identified sites

Easily use identified sites to set up docking models for structure-based virtual screening experiments with Glide.

Explore binding sites to guide ligand design
Explore binding sites to guide ligand design

Use generated binding site maps to guide what types of ligand modifications would be expected to promote binding.

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

Materials Science
Virtual Screening of Soybean Protein Isolate-Binding Phytochemicals and Interaction Characterization
Life Science
Structure-based assessment and druggability classification of protein-protein interaction sites
Life Science
Toward in vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia
Life Science
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Life Science
Driving forces for ligand migration in the leucine transporter
Life Science
Identifying and characterizing binding sites and assessing druggability
Life Science
New method for fast and accurate binding-site identification and analysis
Life Science
A Computational Approach to Enzyme Design: Predicting ‘-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring
Life Science
Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase
Life Science
Improved docking of polypeptides with Glide

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.