fpocket User Manual
fpocket is a protein pocket prediction algorithm. Given a PDB protein
structure it enables the user to identify potent binding sites. Based on
Voronoi tessellation, this algorithm is very fast and particularly well
suited for large scale protein binding pocket screenings and development
of scoring functions for binding pocket characterization. Now, fpocket
also allows pocket detection on MD trajectories and assessment of the
volume & the druggability of a binding site. Last, also interaction
energy calculations are now possible using fpocket & mdpocket.
Notes
- This program uses output coming from Qhull. Qhull is integrated
within fpocket. More information about Qhull can be found in the paper :
Barber, C.B., Dobkin, D.P., and Huhdanpaa, H.T., “The Quickhull
algorithm for convex hulls,” ACM Trans. on Mathematical Software,
22(4):469-483, Dec 1996, http://www.qhull.org
- Part of this software includes code based on external code developed
by the Theoretical and Computational Biophysics Group in the Beckman
Institute for Advanced Science and Technology at the University of
Illinois at Urbana-Champaign. The PDB parser of the Molfile Plugin of
VMD were modified for the purposes of fpocket’s PDB parsing.
Furthermore, the molfile plugin allows now mdpocket to analyse various
MD trajectory formats.
- Within the whole documentation code and output from computer
programs are represented and formatted in the following way :
ls -1 > out.txt
- This documentation, as well as the software itself, is under steady
change. The fpocket developer team tries to provide a useful and easy to
understand documentation, a thing that completely lacks in most of
scientific open source softwares nowadays. In our opinion an open source
software is useless without documentation of the source code on one side
and documentation of the software on the other. Thus, we welcome every
suggestion to improve this documentation in terms of accuracy, clarity
and completeness.
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