Hex Protein Docking

• November 2013 – Hex 8.0.0 now available for Linux-64, Windows, and IntelMac!
• June 2021 – Hex is now distributed by the OneAngstrom company, in the frame of their Samson Platform. Contact them for recent updates or developments.

About Hex

Hex is a very fast protein-protein docking program that was developed by Dave Ritchie. It uses a novel 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.

Hex is an interactive protein docking and molecular superposition program, written by Dave Ritchie. Hex understands protein and DNA structures in PDB format, and it can also read small-molecule SDF files. Between November 2013 and December 2015, there have been over 40,000 downloads.

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.

Download Hex 8.0.0

For Academic and Governmental users, a runtime version of Hex may be downloaded free of charge. You are asked only to comply with a wordy, but mostly harmless, licence agreement. Corporate users may also download the software for evaluation, although prior agreement with the author is required if the program is to be used for profit.

Hex 8.0.0   for Windows and Linux with GPU acceleration (CUDA 5.0), and Mac OS X (link to be updated)

Hex Documentation and Examples

The User Manual (very complete, 70 pages) is included in the software installation, and is also available here.

The basic installation includes some examples. A more extensive set of docking test cases can be obtained from Zhiping Weng’s Docking Benchmark.

Original example images from Hex are available as the « Hex gallery » document (not updated since 2013).

Hex and Sam

The « Sam » (symmetry assembler) program uses the Hex polar Fourier correlation technique to build symmetrical protein complexes with any of the naturally occurring point group symmetries (Cn, Dn, T, O, and I). Check it out! Read more on the Sam software page here.

Citing Hex

• Parametric Protein Shape Recognition, D.W. Ritchie (1998), PhD Thesis, University
  of Aberdeen.
• Fast Computation, Rotation, and Comparison of Low Resolution Spherical Harmonic
  Molecular Surfaces, D.W. Ritchie and G.J.L. Kemp (1999), J. Comp. Chem. 20, 383-
  395.
• Evaluation of Protein Docking Predictions Using Hex 3.1 in CAPRI Rounds 1 and 2,
  D.W. Ritchie (2003), PROTEINS: Struct. Funct. Genet. 52, 98-106.
  http://www.loria.fr/~ritchied/papers/ritchie_capri_paper.pdf
• Protein Docking Using Spherical Polar Fourier Correlations, D.W. Ritchie and G.J.L.
  Kemp (2000), PROTEINS: Struct. Funct. Genet. 39, 178-194.
  http://www.loria.fr/~ritchied/papers/docking.pdf
• Docking Essential Dynamics Eigenstructures, D. Mustard and D.W. Ritchie (2005),
  PROTEINS: Struct. Funct. Bioinf. 60(2), 269-274.
• High Order Analytic Translation Matrix Elements for Real Space Six-Dimensional
  Polar Fourier Correlations, D.W. Ritchie (2005), J. Appl. Cryst. 38, 808-818.
• Toward High Throughput 3D Virtual Screening using Spherical Harmonic Molecular
  Surface Representations, L. Mavridis and D.W. Ritchie, (2007), J. Chem. Inf. Model. 47(5), 1787-1796.
• Recent Progress and Future Directions in Protein-Protein Docking, D.W. Ritchie,
  (2008), Curr. Prot. Pep. Sci. 9(1), 1-15.
• Accelerating Protein-Protein Docking Correlations Using A Six-Dimensional Analytic
  FFT Generating Function, D.W. Ritchie, D. Kozakov, and S. Vajda (2008), Bioinfor-
  matics 24(17), 1865-1873.
• Fast FFT Protein-Protein Docking on Graphics Processors, D.W. Ritchie, and V.
  Venkatraman (2010), Bioinformatics 26(19), 2398-2405,

Please mention also this web page « https://mbi-ds4h.loria.fr/softwaretodownload/hexsoftware/ »

Acknowledgements

Dave Ritchie passed away prematurely on Sept 15, 2019. His open-mindedness and scientific contributions continue to inspire us.

Contact

Sjoerd de Vries
SISR LORIA
Campus Scientifique
BP239
54500 Vandoeuvre-lès-Nancy
sjoerd.devries AT loria.fr