Understanding where and how small molecules bind to a protein is paramount in drug design. Pocket detection enables the exploration of the structural landscape of a target protein, uncovering potential druggable binding sites and providing critical insights that guide early discovery decisions with confidence and precision. Whether working with an X-ray crystal structure, homology model, or dynamic ensembles from a molecular dynamics simulation, identifying and characterizing binding pockets is important when analyzing a protein. In addition to a known orthosteric site this analysis can also highlight alternative regions such as allosteric pockets, opening the door to alternative and innovative drug design strategies.

With pocket detection, you can rapidly analyze a wide variety of binding site types, from well-defined cavities to shallow and hidden pockets that appear only in molecular dynamics simulations, when the protein moves. Each site is scored and described using a comprehensive set of parameters; including druggability, volume, hydrophobicity, and spatial characteristics. These results help prioritize the most promising pockets for downstream workflows such as virtual screening or docking.

By applying pocket detection across molecular dynamics trajectories, it can allow monitoring of pocket flexibility, opening/closing states, and identifying pockets not visible in static structures. Importantly, pocket detection is not restricted to locating surface voids; it also allows identification of functional opportunities to modulate protein behavior, translating structural data into actionable insight, revealing pockets with biological significance, including those that may mediate allosteric regulation or protein-protein interactions.