Please join us for an FFEA practical workshop on the 13th of July, hosted by CCPBioSim, CCP-EM and the University of Leeds.

Features

  • Protein interactions:
  • Kinetic state changes can be simulated together with the continuum model to account for conformational changes and binding events.
  • Conversion tools for EM density data and atomistic structures into FFEA simulations.
  • A plugin for PyMOL, allowing the visualisation of FFEA systems and trajectories.
  • Analysis tools (equilibration, Euler characteristic, principal component analysis, gemoetric measurements) available on the command line and under a Python API.
  • Extensive test suite including checks of FFEA's simulation output against analytical results.

Videos

Coming Soon!

Publications

Technology

  • Boost (>=1.54.0) is used for ease of programming at the initialisation phase. Modules "system", "filesystem" and "program-options" are required. A bundle of version 1.63 is shipped with FFEA.
  • Eigen (>=3.2.1). FFEA uses Eigen to calculate and solve linear approximations to the model i.e. Elastic / Dynamic Network Models. CMake will download and use Eigen 3.3.2 if not told otherwise.
  • RNGStreams is shipped with FFEA and used as Random Number Generator (RNG). RngStreams allows the FFEA to safely generate random numbers when running on a number of threads, as well as safe restarts, recovering the state of the RNGs in the last saved time step.
  • tet_a_tet is shipped with FFEA and used to detect element overlapping in the steric repulsion module.
  • Doxygen (>= 1.8) [OPTIONAL] is used to generate the documentation.
  • PyMOL (>=1.8) can be used, using the plugin we provide, to visualise FFEA systems and trajectories as well as molecular and EM systems.
  • mtTkinter is recommended for stability.
  • GTS (>=0.7.6)[OPTIONAL]. The GNU Triangulated Surface Libraries allowing the manipulation and coarsening of surface profiles.
  • NETGEN or TETGEN [OPTIONAL]. Programs which convert surface profile into volumetric meshes to be used by FFEA.
  • pyPcazip [OPTIONAL] Some of the Python FFEA analysis tools interact with these Principal Component Analysis library in order to generate the standard PCA output (eigensystems, projections, animations etc) obtained from standard from equivalent MD simulations.

Contribute

FFEA is maintained by a small but dedicated team at the University of Leeds. If you want to see where we can take FFEA, then you can:

  • Use the software for something cool
  • Send bug reports and feature requests to our issue tracker
  • Fork us