The identification and characterization of potential druggable binding sites for small molecule ligands is a key step in the molecular modeling of novel targets and lead series.
Pocket detection and analysis in Flare uses fpocket, a fast protein pocket detection algorithm for the identification and characterization of pockets and cavities within a protein structure. It can be run on individual protein structures experimentally derived by X-ray, modeled by homology, or obtained as a snapshot from molecular dynamics studies.
Using the mdpocket extension of the method, pocket analysis can be run or on conformation ensembles from Molecular Dynamics, to monitor the frequency of opening/closing and the druggability of pockets.
- Find the druggable binding sites in your protein
- Search for different types of pockets, including drug binding sites, water binding pockets, channels and small cavities and large solvent exposed sites
- Characterize each pocket according to different parameters, including a druggability score
- Monitor the frequency of opening/closing of druggable binding pockets over a Molecular Dynamics trajectory
