Epock Benchmarks are a set of control and test-case systems which aims at providing some standards for benchmarking pocket volume measurement / pore profile calculation software.

The material is public and available at the Epock benchmark package page.

The repository is contains two subdirectories:

  • control contains artificial systems in which the pocket volume is know
  • test_cases contains biological system trajectories

Control systems

Epock benchmarks thus far contains a single control system, namely sphere. This system is made of a multitude of pseudo-atoms distributed in space in order to create a spherical void at in the middle of the set of pseudo-atoms.

As the equation of the points on a sphere is known and the pseudo-atoms are very closely located, the surface of the resulting void is expected to be as close as possible from a perfect sphere with known radius, therefore known surface.

Test cases

Test cases gather together “real” biological systems containing pockets or channels.

They are useful to evaluate a software performances on real-life problems and to compare raw data provided by different programs.