Welcome to the fpocket web server
Three servers are proposed and accessible from this page (see on the right):
- Fpocket: perform simple pocket detection
- MDpocket: track pockets in molecular dynamics
- Hpocket: view conserved pockets withing homologous proteins
There are actually two version of each server: a default and an advanced version (using Mobyle portal). Both make use of exactly the same protocol, and will return you exactly the same results. Only, the mobyle portal has several advantages over a simple standalone server, like the possibility to bookmark jobs, register as user to store jobs on the server (parameters included), and use pipelining features to transfer F/H/MDpocket output to any other compatible service available in mobyle.
fpocket is a very fast, open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program, and from now as a web server too.
Since its first release, the new package mdpocket has been developped. This package has been designed to track cavities on different, aligned protein structures, and thus can be used to:
- track protein cavities during molecular dynamics trajectories (original goal)
- search for conserved pockets in protein families
Currently available as a web server only, mdpocket will be released in the fpocket official distribution as soon as the corresponding scientific paper will be published.
If you use fpocket for publication, please cite:
Schmidtke P, Le Guilloux V, Maupetit J, Tuffery P, fpocket: online tools for protein ensemble pocket detection and tracking , Nucleic Acids Res. 2010 May 16.
Le Guilloux V, Schmidtke P and Tuffery P, Fpocket: An open source platform for ligand pocket detection , BMC Bioinformatics, 2009, 10:168