Docking
EROS-DOCK: Coarse-grained rigid docking with exploration of 3D rotational space
EROS-DOCK is a coarse-grained docking approach that uses the physics-based ATTRACT scoring function in conjunction with a quaternion « pi-ball » representation of 3D rotational space. The pi-ball allows over 95% of candidate docking poses to be eliminated trivially due to steric clashes, thus allowing the remaining non-clashing orientations to be calculated very efficiently. In this way, the approach combines the exhaustive coverage of classical FFT-based approaches with an « exact » high quality scoring function.
EROS-DOCK was written by Maria Elisa Ruiz Echartea, with some contributions from Dave Ritchie.
Go to the main Eros-Dock web page.
Hex: FFT-based rigid docking
Hex is a very fast protein-protein and protein-ligand docking program developed by Dave Ritchie. It uses a spherical polar correlation technique to accelerate the docking calculations. Hex can exploit highly parallel modern graphics processor units to achieve a further significant speed-up. Overall, Hex is up to three orders of magnitude faster than conventional FFT-based docking algorithms.
Go to the main Hex web page.
3D modelling and superposition
SAM: Assembling using symmetry
Sam is a fast FFT-based protein docking program that has been specifically designed to assemble perfectly symmetrical protein complexes with arbitrary point group symmetry.
Sam was developed by Dave Ritchie and Sergei Grudinin. The project was funded in part by the ANR (Project PEPSI), grant reference ANR-11-MONU-0006.
Go to Sam web page here
Kpax: Superposing protein 3D models
Kpax is a very fast protein structure alignment and database search program, developed by Dave Ritchie.
Go to the main Kpax web page.
Cryo-Electro Microscopy : cryoEM
gEMtools: Tools for processing cryo-EM data
gEMtools is a suite of tools for processing electron-microscopy micrographs using graphics processors to accelerate the calculations. These tools were developed by Thai Hoang during projects funded by the ANR (PEPSI) and Region Lorraine.
Go to the gEMtools main page.
