In order to run a docking calculation, it is necessary to provide two protein structures, and to specify a
few parameters that control the calculation.
Hex calls the two proteins to be docked the "receptor" and "ligand", respectively. These can be uploaded from PDB files on your PC. For most practical purposes, the receptor and ligand are interchangeable although it is conventional to call the smaller protein the ligand. The Hex Server removes all water molecules and other "hetero" atoms from the input files.
During the main docking calculation, Hex rotates each protein about its own coordinate origin, and varies the separation between the two origins. A score is calculated for each orientation, and the highest-scoring orientations are saved and returned to the user.
In general, PDB files may be downloaded from the RCSB Protein Data Bank. Before doing a docking calculation, it is usually a good idea to examine your PDB files using a visualisation tool such as Hex, Jmol, or VMD, and then to use a text editor to delete any duplicate domains or unwanted atoms before docking. It is also strongly recommended to study the relevant literature in order to find information about the possible interface site(s) on one or both proteins. If you can specify a possible interface residue for each protein (step 2: Docking Parameters), you can limit the angular search range, and this will greatly increase the probability of finding a high-ranking near-native prediction in the results list.
The "Correlation Type" entry box is used to specify the type of docking calculation to be performed (shape-only, or shape+electrostatics). Requesting electrostatics can be beneficial if the proteins have complementary formal charges. Electrostatics should not be used when docking DNA or RNA molecules.
The "Calculation Device" entry box is used to request that the calculation will be performed by a graphics processor unit (GPU) or the central processor (CPU). Normally the GPU is much faster that the CPU. Multiple GPUs or CPUs will be used if they are available.
The "Final Search" entry box is used to specify the main expansion order N, although the default value of N=25 is usually sufficient for most purposes. However, performing the full docking calculation with N=25 is time-consuming. In practice, almost identical results are achieved by using a fast initial scan of the orientational search space using N=16, and then rescoring only the top 10,000 orientations with N=25.
If desired, the molecular centroids may be changed using the "Origin Residue" selection boxes. These selection boxes show the list of residues found in each chain of each input PDB file. If a protein residue is selected, the coordinates of its Alpha-Carbon atom will be used as that molecule's coordinate origin.
If some information is known about the binding sites of one or both proteins, it is often worthwhile to limit the range of the docking search to exclude from consideration relative orientations that don't involve the binding epitope(s). Exploiting this kind of information can significantly help to reduce the number of false-positive or incorrect docking predictions. Hex assumes that the centre of each protein's binding epitope is initially located on the intermolecular axis, as indicated in the Docking-Parameters(2/2) page illustration. Hex allows the user to explicitly pre-orient each protein using the notion of so-called Interface Residues. If you specify an interface residue for either the receptor, the ligand, or both using the "Interface Residue" selection box, the corresponding protein will be pre-oriented such that the alpha Carbon atom of that residue is located on the intermolecular z axis.
If the rotational search is then considered in terms of rotating the Interface Residue away from the z axis and onto different angular positions (icosahedral tesselation sample points) about each protein's origin, then the angular search may easily be constrained using a single Range Angle parameter for each protein, which essentially defines a spherical cone centred on the z axis. Only angular samples that fall within the Range Angle cone are used for the docking search. A Rangle angle of 180 degrees corresponds to using no angular constraints, whereas a range angle of 45 degrees would typically be a good choice to loosely limit the search about the starting orientation.
The Step Size is the angular resolution in degrees of each of the five rotational degrees of freedom in the rigid body search space. Angular search increments are generated from two icosahedral tesselations of the sphere: one for the receptor and one for the ligand. The angular coordinates of each tesselation vertex provide one pair of rotational coordinate values. The angular distance between any neighbouring pair of points is approximately equal to the given step size. The fifth angular degree of freedom corresponds to a twist rotation about the intermolecular axis. Twist rotations are normally calculated as a one-dimensional FFT with 64 steps, which correslponds to an angular step size of 5.6 degrees. The Step Size parameter controls only the tesselation size. Normally, the default value does not need to be changed.
If desired, you can request a different number of returned solutions (up to a limit of 1000) using the "Number of Solutions" selection box. If you wish to inspect large numbers of solutions, or if you want more detailed control over the calculations, you are welcome to download the Hex program and run your calculations directly on your own machine.
Once the docking calculation is complete, you will be forwarded to a results page from which (by default) the best 100 solutions will be made available for download as a compressed PDB file. The first 20 docking orientations are also available as uncompressed individual PDB files. If you gave your e-mail address on the Docking Definition page, you will also be sent an e-mail message containing a link to the results page.
For most calculations only the names of the receptor and ligand files need to be given: the default values for the other parameters should normally be sufficient.