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. A GUI is in development and mdpocket (fpocket on md trajectories) is out now. fpocket includes two other programs (dpocket & tpocket) that allow you to extract pocket descriptors and test own scoring functions respectively. Furthermore a nifty druggability prediction score has been added to fpocket recently.
As the algorithm is very fast it can be used on a large scale level (PDB size for instance).
If you use fpocket for publication, please cite :
Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, "Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168

If you use mdpocket for publication, please cite :
Peter Schmidtke, Axel Bidon-Chanal, Javier Luque, Xavier Barril, "MDpocket : Open Source Cavity Detection and Characterization on Molecular Dynamics Trajectories", Bioinformatics, 2011

 

News
already 3765 downloads since the publication
 
3 Oct 2011 We are proud to announce that the MDpocket paper was finally published in Bioinformatics. It is now available as advanced access paper, so people already using MDpocket can now cite that paper as primary reference.
   
May 2011 The fpocket project was invited at the Molecular Informatics Open Source Software 2011 conference in Hinxton among well known open source projects in drug discovery, like Openbabel, Rdkit, CDK, Gromacs and many more. This is a nice confirmation of our increasing user base and that fpocket is becoming a main-player in open source cavity prediction. All presentations including the fpocket presentation can be found on the MIOSS website.
   
27 Jan 2011 The fpocket project crossed the milestone of 1111 downloads since its first publication. Thanks for every user / downloader, we are looking forward for more .... ;)
   
13 July 2010

The druggability score is published and integrated into a brand new fpocket release, fpocket2. Together with this comes a first standalone shot of mdpocket and several bugfixes and improvements in fpocket.
Find out more about the druggability score in the paper published in J Med Chem.

   
29 April 2010

The official fpocket webserver is out. The corresponding paper is freely accessible in the Nucleic Acids Research WS 2010 issue.
The webserver allows you to run basic fpocket runs, but also already includes a first shot of mdpocket. Last another nice and interesting feature was added to the webserver called hpocket, running fpocket on homologous structures to find conserved cavities.

There is lots of documentation and examples available on the webserver, so just have a look ;).

 

 

04 April 2010

Thanks to Alessandro Pedretti, the molecular modelling software for Windows VegaZZ contains now a plugin for fpocket based cavity detection. More information about VegaZZ can be found here.

 

 

09 November 2009

Vincent and me are currently working on the first official release of mdpocket. Mdpocket allows pocket tracking on molecular dynamics trajectories. For knowing when the official release will be scheduled, please subscribe to the fpocket newsletter.

New tutorials and an up to date manual will also be available then.

 

 

05 July 2009

The fpocket development team announces that within a short time a very nice and nifty graphical user interface (JAVA based) will be available within the official release. Until this release you still have to wait a little bit, but feel free to subscribe to the fpocket newsletter in order to stay tuned about new releases.

Furthermore a first draft of a fpocket reference API documentation is available on this website.

 

 

25 June 2009

The developers of fpocket are proud to announce that our fposter (the scientific poster explaining fpocket) won the best poster price at the "Journées Nationales de Chémoinformatique" in Montpellier. This meeting was the annual assembly of the growing SFCI (Société Francaise de Chémoinformatique) which reunited the French chemoinformatics community.

We would like to thank all participants and people who voted for fpocket. You can download the fposter here.

 

 

2 June 2009

The fpaper (paper explaining the fpocket method) submitted to BMC Bioinformatics has been accepted for publication and was published the same day. Take a look at the paper if you want some details about how fpocket does what it is doing best...detecting protein ligand binding pockets : BMC Bioinformatics paper

In order to cite fpocket please use the following references :

Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery,
"Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168

 

fpocket development is supported by

 

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