Protein docking with Hex
In this tutorial, you will see how to perform protein docking with the Hex SAMSON Extension.
The Hex Extension wraps the protein docking program Hex developed by David Ritchie (Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins: Structure, Function, Bioinformatics)
Requirements#
- SAMSON version 2020 R3 or newer
- Hex Extension.
Note
After adding a new extension from SAMSON Connect, it is necessary to restart SAMSON for it to automatically download and install the newly added extension.
First steps#
In SAMSON, go to Home > Download and insert https://www.samson-connect.net/documents/575f78c0-27b9-4f24-bc39-78cf1d52ecc2 - this will load a document with this tutorial's sample from SAMSON Connect.
The sample document contains structural models of two proteins: 2PTC_E and 2PTC_I.
Note
If you cannot see the Document view, you can enable it in the Interface menu or by using the shortcut: Ctrl/Cmd + 1.
Preparation of the system#
Now, we need to prepare the system:
- Remove atoms with alternate locations.
- Remove water, monatomic ions, ligands, if they are present.
- Add hydrogens, if they are not present. Note, that if the system has hydrogens added based on some protonation you shouldn't modify hydrogens.
To do all of this in a single step, go to Home > Prepare and check the above-mentioned options as shown in the image below.
Please note, that the system in the tutorial file has all the water already removed and hydrogens already added.
Tip: remove alternate locations
Alternatively, you can check the system for alternate locations using Home > Validate - this will launch the Structure validation module. There in the Alt. locations tab, click Find alternate locations. If there are any, they will be shown in the table. If there were any it is necessary to remove them by clicking on Remove alt. locations.
You can also perform other checks for your system if necessary, e.g. check bond lengths, non-standard residues, and clashes.
Tip: remove water
Alternatively, you can remove water as follows: click on Select > Water to select it in the document, and then click on the Current selection in the Document view and choose Erase selection in the context menu or click on delete in the pop-up context toolbar.
Tip: remove ions
Alternatively, you can remove monatomic ions as follows: click on Select > Ions > Monatomic ions to select them in the document and then click on the Current selection in the Document view and choose Erase selection in the context menu or click on delete in the pop-up context toolbar.
Tip: add hydrogens
Alternatively, you can add hydrogens to a system using Edit > Add hydrogens - this will add hydrogens for the standard pH based on amino acid types and valences. To add hydrogens to only to a part of the system, select this part and then click on Edit > Add hydrogens. Note, that we don't necessarily need to minimize the structure after adding hydrogens since AutoDock Vina needs only polar hydrogens for determining hydrogen bonds.
Tip: visualization
If you don't have secondary structures shown, you can add them for each of the two proteins by first selecting their structural model in the Document view and then clicking on Visualization > Visual model > Ribbons.
You can hide/show the atomistic representation by toggling the boxes in front of the protein structure in the Document view.
To learn more about visual models in SAMSON please follow interactive tutorials in SAMSON (Help > Tutorials) or the User guide: Visualizing tutorial.
Setup of the system#
Open the Hex app via Home > Apps > Biology > Hex. You can also find it using the Find everything... search box in top menu of SAMSON - just start typing the name.
Let's now set one protein as the receptor and another one as the ligand. Select the 2PTC_E protein in the document and click "Set" as the receptor. Select the 2PTC_I protein in the document and click "Set" as the ligand.
Let's save the initial ligand conformation. For that, select the ligand, 2PTC_I, in the document and click Edit > Conformation. This will be useful if you want to redo the docking with different parameters for the same initial conformation.
Hex parameters#
Below is a brief description of the main Hex parameters. To learn more about them and other parameters please see their tooltips in the Hex interface and the Hex manual. Below we list some of the main parameters.
You can always reset parameters to their default values by clicking on the "Reset parameters" button.
Correlation type#
The Correlation type is used to specify the type of docking calculation to be performed (Shape-only, Shape + electrostatics, etc). Requesting electrostatics can be beneficial if the proteins have complementary formal charges. Electrostatics should not be used when docking DNA or RNA molecules.
Sampling method#
Choose the type of sampling method. It is used to restrict the docking search.
Range angles#
The docking search may be restricted by defining range angles for the receptor and/or ligand orientations. If range angles are defined, then the interface residues will always be constrained to appear within a spherical cone (with its axis being an intermolecular axis between origins of both proteins) defined by the corresponding range angle. You can define the range angles in the Advanced parameters. If the interface residues of a receptor or a ligand are known you can orient them pointing at each other and limit the receptor and ligand range in the Advanced parameters to reduce the number of false-positive or incorrect docking predictions and to reduce the search time.
See below how to specify the range angles in the Setup of the search domain section.
Post-processing#
Following the basic docking correlation algorithm, candidate docking orientations may be filtered and refined using one of the Post-processing options. Post-processing is applied to the user-selected number of top-scoring solutions from the correlation search.
Bumps counts#
The simplest option is to enable a bumps counter, in which the number of steric clashes between non-bonded pairs of heavy atoms in each solution is calculated. An option in the Results table may then be used to filter out solutions with a specified number of steric clashes.
Molecular Mechanics Refinement#
This is in an alpha stage in Hex. In addition to the bumps counter, a single (rigid body) molecular mechanics energy may be calculated for each docking solution (MM Energies), or a Newton-like energy minimization (MM Minimisation) can be applied to each docking solution. These energies are calculated using "soft" Lennard-Jones and hydrogen bond potentials, adapted from the OPLS forcefield parameters, along with an explicit charge-charge electrostatic contribution. When docking complexes where conformational changes are known to be small, this gives an effective way to prune many "false-positive" orientations and to enhance the energy of the "right answer". However, this rigid-body refinement procedure should not be used if conformational changes are expected to be large because (despite using soft potentials) it tends to eject ligands with incorrect conformations from the binding site.
Steric scan#
Performs the fast low-resolution Steric scan phase before the high-resolution Final search. Hex performs the high-resolution Final search correlation using smaller distance increments than are used for the fast low-resolution Steric scan phase. This allows the search space to be covered more rapidly (coarsely) in the first phase, but more finely in the final phase.
Together with the Final search, this allows the search space to be covered more rapidly (coarsely) in the first phase (the Steric scan phase), but more finely in the final phase. The Steric scan order equal to 16-18 should be sufficient in most of the cases.
In this mode, about all but the top 10,000-30,000 orientations (depending on other advanced parameters) are discarded after the Steric scan. The Steric scan may be toggled off, in which case every orientation is evaluated using a steric correlation (and optionally an electrostatic correlation) to order N, as given the Final search slider. However, this can significantly increase total docking times. Using the two-step search with N=16 for Steric scan and N=25 for Final search (or N=20 for Steric scan and N=30 for Final search) is found to work well in practically all cases.
See also the Final search parameter.
Final search order#
This is the order of 3D expansion. The Final search order should be higher than the Steric scan order if the Steric scan is used. Hex performs the high-resolution Final search correlation using smaller distance increments than are used for the fast low-resolution Steric scan phase.
This 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. Generally, N=30 is recommended when docking high-resolution crystal structures for which the conformational change on the binding is expected to be small. N=25 should be used when docking model-built structures or structures which are expected to be more flexible.
Setup of the search domain#
The Sampling method needs to be set to Range angles.
To specify the search area (range angles), click on Advanced parameters.
In Hex the docking search is done in spherical coordinates and the search domain is determined by the rotational angles of the receptor and the ligand around the intermolecular axis that connects centers of the receptor and the ligand. By default, the angles are set to 180 degrees meaning that the whole sphere of the molecule is accessible to the search. Please note that only the ligand is rotated and positioned around the receptor.
If you already know the location of the binding site, you should manually move and orient the ligand to be close to the binding site and then restrict the receptor rotation angle range to a small value, say 45 degrees. This should limit the search domain and improve the search time. To align (translate and rotate) the ligand towards the receptor you can use one of the Move editors.
Range angles of the receptor and the ligand: In the case of the rotational search - the sampling method is set to range angles - the angular search may easily be constrained using the Range angle parameter for each protein, which essentially defines a spherical cone centered on the intermolecular axis that goes through the origins of both proteins. Only angular samples that fall within the Range Angle cone are used for the docking search. A Range 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.
Twist angle range: A twist rotation about the intermolecular axis (an axis between origins of the proteins).
Let's now specify the receptor angle range and the ligand angle range. Set the receptor angle range to 45 degrees and the ligand angle range to 45 degrees. You should see two cones with their apexes placed in the centers of two proteins and an axis connecting the centers of two proteins.
In the same way, you can limit the twist rotation angle of the ligand about the intermolecular axis.
Running the docking#
Once you specified the necessary parameters click on the Run docking button. For the system in the tutorial the docking should take about several minutes.
Tip
To see logs start the Log viewer module (Home > Apps > All > Log viewer).
Results#
Once the docking search is done, you can view the results in the Results tab. The modes are clustered together and you can view either the best mode (the lowest energy solution) per cluster or all the modes.
By clicking on a row in the table the corresponding conformation of the ligand will be restored. You can also export this conformation in the document by right-clicking on the row[s] and choosing Create conformation.
You can also launch an animation of all the modes at the bottom of the Results tab. In the gif below, we have applied the Gaussian surface to the receptor and colorized it based on the residue hydrophobicity.
Performing further analysis#
SAMSON provides different tools to perform analysis of the results. You can add various visual models, measure distances, compute some parameters, and check for ligand-receptor interactions. Below you will find some examples.
The Protein-Ligand Interaction Analyzer Extension allows for computing the contact area, H-bonds between a ligand and a receptor, ligand surrounding residues, and some other parameters.
The Hydrogen Bond Finder Extension allows one to find and visualize hydrogen bonds (H-bonds) inside a molecule or between molecules, e.g. between a ligand and a receptor. To find H-bonds between a ligand and a receptor, select the second option ("... in the current selection and the system"), then select the receptor and click on the "Set" button, modify parameters if necessary (you can later modify them in the created H-bond visual model using the Inspector), then select a ligand and click on the Add hydrogen bond visual model button.
Please see the AutoDock Vina Extended tutorial - Performing analysis for more details on different tools for analysis.
That's all, thank you for completing this tutorial on the Hex Extension. Please do not hesitate to write on our Forum if you have any questions or feedback.