Section: New Software and Platforms

Hex

Keywords: 3D rendering - Bioinformatics - 3D interaction - Structural Biology

Scientific Description The underlying algorithm uses a novel polar Fourier correlation technique to accelerate the search for close-fitting orientations of the two molecules.

Functional Description Hex is an interactive protein docking and molecular superposition program. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule “SDF” files. Hex will run on most Windows-XP, Linux and Mac OS X PCs. The recent versions now include CUDA support for Nvidia GPUs. On a modern workstation, docking times range from a few minutes or less when the search is constrained to known binding sites, to about half an hour for a blind global search (or just a few seconds with CUDA). On multi-processor Linux systems, docking calculation times can be reduced in almost direct proportion to the number of CPUs and GPUs used. The calculations can be accelerated by using an optional disc cache (strongly recommended) of about 1 GB of disc space.

• Participant: David Ritchie

• Contact: David Ritchie

• URL: http://hex.loria.fr