harryjubb / fpocket

Fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in an industrial setting and require official support, please contact Discngine (www.discngine.com).

fpocket project

The fpocket suite of programs is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level.

Content

fpocket: the original pocket prediction on a single protein structure mdpocket: extension of fpocket to analyse conformational ensembles of proteins (MD trajectories for instance) dpocket: extract pocket descriptors tpocket: test your pocket scoring function

What's new compared to fpocket 2.0 (old sourceforge repo)

fpocket:

• is now able to consider explicit pockets when you want to calculate properties for a known binding site
• cli changed a bit
• pocket flexibility using temperature factors is better considered (less very flexible pockets on very solvent exposed areas)
• druggability score has been reoptimized vs original paper. Yields now slightly better results than the original implementation.
• compiler bug on newer compilers fixed mdpocket:
• can now read Gromacs XTC, netcdf and dcd trajectories
• can also read prmtop topologies
• if topology provided, interaction energy grids can be calculated for transient pockets and channels (experimental)

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

The most recent versions (starting with fpocket 3.0) make use of the molfile plugin from VMD. This plugin is shipped with fpocket. However, now you need to install the netcdf library on your system. This is typically called netcdf-devel or so, depending on you linux distribution. fpocket needs to be compiled to run on your machine. For this you'll need the gnu c compiler (or another one, but didn't test with others than GCC). install netcdf-devel on ubuntu type :

sudo apt-get install libnetcdf-dev

on a RHEL based distribution something like this should do:

sudo yum install netcdf-devel.x86_64

Installing

Download the sources from github via the website or using git clone and then build and deploy fpocket using the following commands.

git clone https://github.com/Discngine/fpocket.git .
cd fpocket
make 
sudo make install

End with an example of getting some data out of the system or using it for a little demo

Running the tests

The source code of fpocket is shipped with samples. They can be found in the data/sample folder. Try to run fpocket against the 1uyd sample to check if it's running OK.

cd data/sample
fpocket -f 1UYD.pdb

fpocket should state when it's beginning to search pocket and also when it's ending the search. Upon completion the folder should now contain a folder called 1UYD_out. Check whether the folder exists and the pdb files contain data and the pocket info file contains results.

User Manual

For now the user manual (still the one from fpocket 2.0) can be found in the doc folder. When I have some time to kill (or if somebody else has) we could add that here somewhere.

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Authors

• Peter Schmidtke - Initial work - pschmidtke
• Vincent Le Guilloux - Initial work - leguilv

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• to be filled