Hex Protein Docking

Hex is an interactive protein docking and molecular superposition program, written by Dave Ritchie. Hex understands protein and DNA structures in PDB format. Version 5.0 can also read small-molecule SDF files.

• Hex Gallery (Graphical Overview)

Hex will run on most Windows-XP, Linux and Mac OS X PCs. The latest Intel and PowerPC versions were built using Fedora 8. Earlier Intel PC versions are available for Fedora Core 4 and 6, RedHat 9, and Ubuntu 7.01. Please note: Hex does NOT work on Intel Mac PCs. Binaries for earlier versions are available for Sun and Silicon Graphics workstations.

On a modern PC, docking times range from a few minutes when the search is constrained to known binding sites, to about half an hour for a blind global search. On multi-processor Linux systems, docking calculation times can be reduced in almost direct proportion to the number of CPUs used. The calculations can be accelerated by using an optional disc cache (strongly recommended), which can consume up to 250Mb of disc space.

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. As of April 2008, there have been 12,000 downloads.

Hex 5.1 (for Windows-XP + Mac OS X + Linux)

The User Manual is included in the software installation, and is also available here:

• Hex User Manual (HTML)
• Hex User Manual (PDF)

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

If you wish to try Hex without downloading the actual program, please use the link below to access the on-line docking server. A typical docking job takes about 5 minutes on our server.

Hex Server

• Hex Server Administrator Page

• Hex Docking Movie (best 100 antibody/lysozyme orientations).

So how good is Hex, or any other docking algorithm for that matter? The CAPRI (Critical Assessment of Prediction of Interactions) experiment aims to answer that question. Since the summer of 2001, Hex has taken part in all of the blind prediction rounds of CAPRI, in which the task was to predict the structures of protein complexes whose structures were in the process of being solved by X-ray crystallography. There are now two special editions of Proteins which describe the algorithms and results: Vol 52(1), July 2003, and Vol 60(2), Aug 2005. Overall, in Rounds 1-2 Hex did quite well, scoring 2 close hits for two of the seven targets. In Rounds 3-5, Hex scored a 1.8A RMS hit at rank 6 for target 12 (cohesin/dockerin) and got some further low to medium accuracy hits for targets 10, 11, 12 and 13, but missed the rest!

There is now an on-going Call For Targets for further prediction experiments. If you are a crystallographer in the process of solving the structure of a protein (or DNA) complex, please consider submitting it as a CAPRI target!

Planet Hex has been orbiting somewhere between the earth and the moon since 1999. Have you discovered planet Hex yet?

Hex is also being used to illustrate protein structure in Second Life by Andrew Lang and Jean-Claude Bradley. Please see: Second Life Chemistry and Hiro Sheridan Photos.

The following publications describe the basic algorithms and some results obtained with Hex:

• Accelerating and Focusing Protein-Protein Docking Correlations Using Multi-Dimensional Rotational FFT Generating Functions D.W. Ritchie, D. Kozakov, and S. Vajda (2008). Bioinformatics. In Press.
• High Order Analytic Translation Matrix Elements For Real Space Six-Dimensional Polar Fourier Correlations, D.W. Ritchie (2005) J. Appl. Cryst. 38, 808-818 .
• Docking Essential Dynamics Eigenstructures, D. Mustard and D.W. Ritchie (2005) PROTEINS: Struct. Funct. Bioinf. 60(2) 269-274.
• Evaluation of Protein Docking Predictions Using Hex 3.1 in CAPRI Rounds 1 and 2, D.W. Ritchie (2003) PROTEINS: Struct. Funct. Genet. 52(1), 98-106.
• Protein Docking Using Spherical Polar Fourier Correlations, D.W. Ritchie & G.J.L. Kemp (2000) PROTEINS: Struct. Funct. Genet. 39, 178-194.
• Fast Computation, Rotation, and Comparison of Low Resolution Spherical Harmonic Molecular Surfaces, D.W. Ritchie & G.J.L. Kemp (1999) J. Comp. Chem. 20(4), 383-395.
• Parametric Protein Shape Recognition, PhD Thesis, D.W. Ritchie, Departments of Computing Science and Molecular & Cell Biology, University of Aberdeen (1998).

For a recent review about the general field of protein docking, please see:

• Recent progress and future directions in protein-protein docking D.W. Ritchie (2008). Curr. Prot. Pep. Sci. 9(1), 1-15.

Much of the early development of Hex was done during projects funded by the BBSRC. Currently, the main source of funding is the ANR.