PockFlex: A web server for analyzing protein binding pockets across structural ensembles

Summary

PockFlex is a web server that analyzes protein structural ensembles to identify, characterize, and prioritize binding pockets (cavities where molecules can bind). It works with data from molecular dynamics simulations, experimental structures, or protein structure predictions. The tool detects pockets in each protein conformation independently, filters those overlapping a user-defined region of interest, and groups similar pockets across the ensemble using residue-level clustering. This enables researchers to study flexible binding sites in proteins, which is important for drug discovery and understanding protein function.