Journal of Cheminformatics | VOL. 14

FPocketWeb: protein pocket hunting in a web browser

Publication Date Aug 26, 2022


Detecting macromolecular (e.g., protein) cavities where small molecules bind is an early step in computer-aided drug discovery. Multiple pocket-detection algorithms have been developed over the past several decades. Among them, fpocket, created by Schmidtke and Le Guilloux, is particularly popular. Like many programs used in computational-biology research, fpocket requires users to download and install an executable file. That file must also be run via a command-line interface, further complicating use. An existing fpocket server application effectively addresses these challenges, but it requires users to upload their possibly proprietary structures to a third-party server. The FPocketWeb web app builds on this prior work. It runs the fpocket3 executable entirely in a web browser without requiring installation. The pocket-finding calculations occur on the user’s computer rather than on a remote server. A working version of the open-source FPocketWeb app can be accessed free of charge from


Computer-aided Drug Discovery Web Browser Computational-biology Research Command-line Interface Remote Server Version Of App Early Step Prior Work Protein Cavities Multiple Algorithms

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