Protein docking with Hex

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In this tutorial, you will see how to perform protein docking with Hex SAMSON Extension.

The Hex SAMSON Extension wraps the protein docking program Hex developed by Dave Ritchie (Protein Docking Using Case-Based Reasoning. A.W. Ghoorah, M. Smail-Tabbone, M.-D. Devignes, D.W. Ritchie, (2013). Proteins: Structure, Function, Bioinformatics)

Content

Requirements

  • SAMSON version 2020 R3 or newer
  • Hex SAMSON Extension. 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.
  • Please download the 2PTC archive which contains protein-protein complex used in this tutorial.

First steps

Launch SAMSON and open the 2PTC.sam file provided in the attached archive. It will open 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.

Validation of the system

First, we need to check the system for alternate locations. For that, go to Biology menu > Prepare > Structure validation – this should open a module as in the image below.

Please note, that to use the Structure validation functionality you need to have at least the Standard plan – you can subscribe to the trial period on SAMSON Connect – Plans. In this tutorial example, the system has already been prepared and there is no need to use the Structure validation module, so if you don’t have access to it you can simply skip to the next section.

In the Alt. locations tab, click on the Find alternate locations button. If there are any, they will be shown in the table. In this tutorial example, there are no alternate locations, but if there were any it would be necessary to remove them by clicking on the Remove alt. locations button. You can also select which alternate locations to delete.

You can also perform other checks for your system if necessary, e.g. check bond lengths, non-standard residues, and clashes.

Preparation of the system

Now, we need to prepare the system:

  1. Remove water.
  2. Add hydrogens, if they are not present. Note, that if the system has hydrogens added based on some protonation you shouldn’t modify hydrogens.

Please note, that the system in the tutorial file has all the water already removed and hydrogens already added, so you don’t need to remove water and add hydrogens.

To remove water, click on Biology menu > Select > Water to select the water structures and atoms in the document and then click on the Current selection in the Document view and choose Erase selection in the context menu.

To add hydrogens to a protein, click on Biology menu > Prepare > Add H by res. type – this will add hydrogens to the system for the standard pH based on amino acid types.


For the visualization purpose, let’s now add a secondary structure visual model for each of the two proteins. In the Document view, select the 2PTC_E structural model and then go to Visualization menu > Add visual model (Ctrl/Cmd⌘ + Shift + V) and select the secondary structure visual model. Repeat the same for the 2PTC_I structural model as well. You can also add a secondary structure visual model for the selection in one click by clicking on Biology menu > Visualize > Secondary structure.

Now you can hide the 2PTC_E and 2PTC_I structural models by unchecking them in the Document view.

If you want to learn more about visual models in SAMSON please follow interactive tutorials in SAMSON (Help menu > Tutorials) or the User guide: Visualizing tutorial.

Setup of the system

Let’s now open the Hex app by clicking on it in the Apps > Biology menu. You can also find it using the Find commands, apps, and editors… search box in the top-right corner 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, right-click on the ligand in the document (2PTC_I) and choose Store 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 a “range angle” 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 counter
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.docking time.

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 dockin button. To see logs start the Log viewer module (Apps > All > Log viewer). For the system in the tutorial the docking should take about several minutes.

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 SAMSON 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 SAMSON 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 SAMSON Extension. Please do not hesitate to write on our Forum if you have any questions or feedback.

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