Docking ligands and libraries of ligands with AutoDock Vina Extended

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In this tutorial, you will see how to dock ligands or libraries of ligands into proteins with AutoDock Vina Extended SAMSON Extension and how to visualize and analyze the results.

The AutoDock Vina Extended SAMSON Extension wraps the popular protein-ligand docking program AutoDock Vina (O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461) and extends its functionality by providing the possibility to:

  • easily set up the system (a receptor, a ligand, or a ligand library), including flexible side chains, rotatable bonds, types of locked bonds;
  • easily set up the search domain based on the receptor, a ligand, or a binding site, or by manually adjusting it in the Viewport or in the interface;
  • specify multiple advanced parameters;
  • perform docking, re-scoring, or generate the project to run it on your cluster;
  • filter the results;
  • save the results, including automatic export of each mode into a separate MOL2 file;
  • analyze the results, export results table, plots;
  • load the previously computed results.

Content

Requirements

  • SAMSON version 2020 R3 or newer
  • AutoDock Vina Extended 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 2AZ8 tutorial archive which contains protein-ligand complex used in this tutorial and a sample ligand library.

First steps

Launch SAMSON and open the 2AZ8-tutorial.sam file provided in the archive. It will open structural models of a protein (2AZ8-A and 2AZ8-B) and of a ligand (2AZ8-IA) bound to the protein – for the sake of the tutorial the protein is put in the “Receptor” folder and the ligand is put in the “Ligand” folder.

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. This step is optional since water molecules will not be considered by AutoDock Vina Extended.
  2. Add hydrogens, if the system doesn’t have them set since AutoDock Vina needs polar hydrogens to determine hydrogen bonds (H-bonds). 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. To add hydrogens to a ligand, select the ligand in the document and click on Biology menu > Prepare > Add hydrogens – this will add hydrogens based on valences. 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.

 

For the visualization purpose, let’s now add a secondary structure visual model for the receptor. In the Document view, select 2AZ8-A and 2AZ8-B structural models and then go to Visualization menu > Add visual model (Ctrl/Cmd⌘ + Shift + V) and select the secondary structure visual model. 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 2AZ8-A and 2AZ8-B 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 AutoDock Vina Extended 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.

Now we need to set up the system:

  1. a receptor;
  2. [optional] receptor’s flexible side chains;
  3. a ligand or a ligand library.

Setup of the receptor

Select the receptor – 2AZ8-A and 2AZ8-B structural models – in the Document view and then click on the Set button in the Set receptor part. You will see the search domain set based on the receptor and its box shown in yellow in the Viewport.

If you want to unset the receptor then just clear the selection and click on the Set button.

Setup of the receptor’s flexible side chains

The setting of flexible side chains allows performing docking to a relatively flexible receptor with rotatable side chains. Note, that having flexible side chains may result in more realistic docking but significantly increases the docking time.

For simplicity, in this tutorial, we will not be specifying flexible side chains. But below you can find how to set up the receptor’s flexible side chains.

You can specify receptor’s flexible side chains using one of the following ways:

  • Select them in the Document view.
  • Select them in the Viewport by switching the Selection filter in the top-left corner of the Viewport to Residues and selecting residues one-by-one using Ctrl and Alt button to add/remove to the current selection. You will need to have the structural model visible in the Viewport. Please see the User guide: Selecting or one of the interactive tutorials in SAMSON.
  • If you have a bound ligand and you want to specify residues around it as flexible, then select this ligand and go to Biology menu > Select > Binding site and specify parameters as necessary and click Ok:

Once residues with flexible side chains are selected, click on the associated Set button in the Set receptor part.

Once you set up flexible side chains, you will see in the Viewport the rotatable bond controllers represented by green cylinders superimposed with bonds. By clicking on them you can switch the bonds from rotatable to not and back (green – rotatable, red – not rotatable). See more about it in the Setup of rotatable bonds section.

Setup of a ligand or a ligand library

The AutoDock Vina Extended allows you to dock either a ligand or a library of ligands.

Setup of the ligand

Let’s first see how to set up a ligand. First, check the Single ligand in the Set ligand part, then select the ligand – 2AZ8-IA – in the Document view and click on the associated Set button in the Set ligand part.

Setup of rotatable bonds

Once you set up a ligand you should see in the Viewport the rotatable bond controllers represented by green cylinders superimposed with bonds. Zoom in on the ligand (select the ligand in the Document view and then press Shift + Space).

By clicking on these controllers you can activate or deactivate these rotatable bonds – switch the bonds from rotatable to not and back – they will change colors when you switch their state. Green means the bond can rotate, and red means the bond cannot rotate. Note, that having rotatable bonds may result in more realistic docking but increases the docking time.

You can also use the option to lock specific bond types (make them non-rotatable). For that, click on the Locked bonds settings and check the types of bonds that you want to be non-rotatable (locked) and click Ok.

Then check the Lock specific ligand bonds option.

Please note the following:

  1. Ligands should either be already minimized or minimization should be applied (see the Minimization of ligands section below). Locking of bonds does not affect minimization i.e. the locked bonds will be rotatable during minimization.
  2. Cis-trans isomers will not be generated so it is necessary to provide all relevant cis-trans isomers in the ligand library.

Setup of the ligand library

In this tutorial, we will be docking not a single ligand but a ligand library, which is provided in the same archive. It is a small sample library with some random ligands obtained from the ZINC library.

In the library, you can provide files of different formats (e.g. MOL2, SDF) and multiple ligands per file.

To dock a ligand library, check the Ligand library option and click on the button to browse the directory with the ligand library.

Note, that by default all the ligands in the library will be considered fully flexible (meaning that all the rotatable bonds will be active). You can lock specific bond types thanks to the aforementioned Lock specific ligand bonds option (first, verify the Locked bonds settings). Please, see the Setup of the rotatable bonds section.

Minimization of ligands

If you want to minimize ligands before docking, which might be necessary in some cases, for example, if ligands in the library are in 2D, then check the Minimize option and choose the preset (the maximum number of minimization steps and stopping criteria). Check the “Add missing hydrogens” option if ligands don’t have hydrogens already set – hydrogens are necessary for detecting bond types during the minimization and polar hydrogens are necessary for docking.

The minimization is stopped based on some stopping criteria – when either the energy difference between steps is less than some threshold during at least some consecutive minimization steps or the maximum number of minimization steps has been reached. These values are determined from the minimization preset.

Setup of the search domain

The next step is to set up the search domain. By default, the search domain is determined once you set the receptor based on the whole receptor. If you already know the binding site you can specify the search domain that surrounds it – this will not only limit the search domain but will also lead to performing fewer computations decreasing the overall docking time.

Note, if you want to hide/show the search domain in the Viewport, then toggle the Show box option.

You can set up the search domain using one of the following ways:

  • Modify the center and the size of the domain in the interface.
  • Adjust the search domain box directly in the Viewport thanks to the controllers placed in the corners of the yellow search box visible in the Viewport – just press on the sphere in the corner of the box and drag it to modify its position.
  • Set it up based on the current selection: select nodes and choose the Based on pocket/selection option from the list and click Set.
  • Set it up based on the bound ligand/binding pocket: select the bound ligand and go to the Biology menu > Select > Binding site, after the binding site is selected choose the Based on pocket/selection option from the list and click Set. See the example below.

You can always just the search domain directly in the Viewport thanks to the search box controllers.

Let’s set up the search domain based on the binding site of the 2AZ8-IA bound ligand. Select the 2AZ8-IA ligand in the Document view and go to Biology menu > Select > Binding site and specify parameters as shown in the image below and click Ok:

This should select residues around the ligand. Now choose the Based on pocket/selection option from the list and click Set.

Please note, that the search domain is set in the global XYZ coordinates. If you want, you can always rotate or align the system using the Move editors to better align the binding site in the global XYZ coordinates.

Running the docking and more

The next step is to run the docking!

The Dock part provides the following options:

  • Dock – performs docking.
  • Score only – performs scoring of ligands in their current positions without minimization.
  • Local optimization only – performs local optimization only and scores ligands in their current positions.
  • Generate PDBQT files only – generates a project with PDBQT files for the receptor and ligands, and a configuration file – you can use this files to launch Vina computations on your own cluster. If the minimization option has been checked, the ligands will be minimized before generating PDBQT files. In the case of the using of a ligand library, the PDBQT files for ligands will be generated with keeping the same hierarchy as in the ligand library.

Choose the Dock from the list since we want to perform the docking.

Now set the exhaustiveness parameter and the maximum number of modes wanted:

  • Set the Exhaustiveness parameter (the higher the better, but the longer the search) to 8.
  • Set the Modes parameter (the maximum number of modes returned by the search algorithm) to 20.

You can also check out the Advanced options where you can modify e.g. the energy range for the resulting modes or weights of the Vina scoring function. We do not advise modifying the weights, if you modified them you can always restore their default values by clicking on the Restore default values button.

If you want your results to be automatically saved on a disk then check the Save results option and select the directory where you want your results to be saved. This will create a project directory with a timestamp in its name, this directory will contain the receptor and ligand files, generated PDBQT files, docked PDBQT files, and MOL2 files for each ligand’s mode. You can later load these results back to AutoDock Vina Extended (see the Loading previously computed results section). Please note, that you shouldn’t modify the hierarchy of the project directory or remove files if you want to be able to load them back in AutoDock Vina Extended.

Please check the Save results option and select the directory where you want your results to be saved. We will need these saved results in the Loading previously computed results section.

Now, press the Dock library button and wait for the results – it should take a couple of minutes. There might be some pop-up dialogs asking for options to import ligands from the library folder. If you are docking a ligand library you can always pause, resume, or stop the computations – the pause and stop will be applied only after the computations for the current ligand are finished.

Visualizing results

As soon as the computations are done, a new folder with the results should be added to the document containing the following:

  • A note called “Configuration” with the docking parameters. If you want to see the note with the docking parameters, right-click on it and choose Inspect in the context menu.
  • A subfolder called “Top ligands” with structural models of the top binding ligands (with the best ranked pose already displayed).
  • Top conformations of the top ligands allowing you to display poses of these ligands.

To restore a conformation either double-click on it in the Document view or right-click on it and in the context menu choose Restore conformation.

You can also create structures (structural models) from conformations, which makes it easier to see clusters of conformations. To achieve this, right-click on one or more conformations and choose “Create structural models from conformations”. This will create structural models for all selected poses, so you can see where clusters are.

Note, that you can hide structural models from displaying in the Viewport by unchecking them in the document.

Note, that all the conformations are stored in a directory with results if you choose to save the results, or if you loaded the previously computed results. You can also export the selection, for example as MOL2 or PDB files, by clicking on Home > Select > Export (Ctrl / Cmd + E). To export the ligand’s conformation in a separate file, restore this conformation by double-clicking on it and then select the ligand’s structural model and click the Export button in the Home > Select menu.

The Results tab in the AutoDock Vina Extended allows you to see the results table and plot, filter the results based on some parameters (e.g. name, affinity, RMSD, etc), export the results table in a CSV file, export the affinity vs compounds plot as an image or in a CSV file. There is a horizontal splitter line between the results table and the plot by dragging which you can modify the size of the results table and the plot.

The results table allows you to sort by columns, copy the data, select ligands and conformations, restore conformations, and export in the document ligands and conformations that are not present among the top ligands and conformations. To do that, right-click on a row and choose a corresponding action from the context menu.

The plot allows for selecting and restoring conformations. By clicking on a data point corresponding to a conformation present in the document, this conformation will be selected in the Document view and vice versa. By double-clicking on a data point, the corresponding conformation, if present in the document, will be restored.

You can use the filter to modify what is shown both in the results table and in the plot.


Loading previously computed results

You can load the previously computed results obtained with AutoDock Vina Extended using the Load functionality in the Results tab. Please note, that you shouldn’t modify the hierarchy of the project directory or remove files if you want to be able to load them back in AutoDock Vina Extended. There are several options to load the results:

  • Only the table of results (fast) – loads only the table of results without loading molecules and conformations. Ligands and their conformations can be loaded later from the results table.
  • Top ligands – loads results (molecules and conformations) only for the specified number of top ligands (by score). The other ligands and their conformations can be loaded later from the results table.
  • Select results to load – loads results (molecules and conformations) only for the selected ligands – a pop-up dialog will appear from which you can select the results to load. The other ligands and their conformations can be loaded later from the results table.
  • All results (slow) – loads all the modes for all the ligands. Please note that it might take time to load docking results for a big ligand library.

Let’s now try to load the results that we just computed. Open a new document (Ctrl + N). Click on the Load button and navigate to the directory with the results:

In the next pop-up dialog, select from the list the Select results to load and check the Load score results for other ligands option to load score results for the non-selected ligands in the results table as well.

Another dialog should appear with a list of ligands found in the results directory. You can deselect all of them by clicking on the Deselect all button and then check the ones which you want to be loaded. Please note that loading results for many ligands might take some time. You can later load the other ligands and their conformations from the results table (see below).

A new folder with the results should appear in the document containing two subfolders:

  • “Receptors” with a receptor and groups with flexible residues and side chains if they were specified.
  • “Docked ligands” with subfolders for each loaded ligand each containing a ligand and its conformations.

If you don’t see the loaded receptor or ligands in the document please make sure that their structural models are checked in the Document view as shown in the image below.

You can load results for other ligands in the results table by right-clicking on a ligand for which you want to load the results and choosing Load ligand results from the context menu. This will load the ligand and its conformations in a subfolder with the ligand’s name in the “Docked ligands” folder.

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.

Visualizing

Let’s first add some visual models for the system. You can learn more about the visualization in SAMSON thanks to the interactive tutorials (Help menu > Tutorials) or to the User guide: Visualizing.

First, select the receptor and add a secondary structure visual model to it using Biology menu > Visualize > Secondary structure. This should add a new secondary structure visual model to the document.

A hint: if you want to hide a visual model simply uncheck it in the Document view; if you want to remove it then right-click on it and choose Erase from the context menu.

Let’s now add labels and a licorice visual for residues surrounding the ligand. First, we need to select residues surrounding the ligand. For that, select the ligand and click on Biology menu > Select > Binding site and set the parameters as in the image below and click Ok. This will select the residues surrounding the currently selected ligand.

You can save this selection in a group by clicking on the Current selection button in the Document view and clicking on Create group in the context menu or on Home menu > Select > Group.

While having these residues selected, click on the Home menu > Edit > Label editor and then click on the Current selection button in the Document view and choose Label selected… > Residues from the context menu. This will add in the document a new folder called “Residue labels”. You can easily hide labels by either unchecking them in the document or by deleting them. Switch back from the Label editor to the default Select editor by clicking on Home menu > Select > Select .

Let’s now add a licorice visual for these residues. While having these residues selected, go to the Visualization menu and click on the Licorice button – this will add a licorice visual model for the selected residues.

If you want, you can colorize carbons in the receptor based on e.g. the residue sequence number. For that select the receptor and go to Biology menu > Select > Atoms > Carbons.

This will select all carbons in the current selection. Let’s now colorize them by the residue sequence number such that their color would correspond to the default style of secondary structure colorization. For that, choose from the Biology menu > Colorize menu the Sequence number option. This should colorize both the carbons in the receptor’s structural model and in the added licorice visual model since the licorice visual model doesn’t have a specific color scheme applied to it.

Now let’s hide the receptor’s structural model by unchecking it in the document. In the end, you should see something like in the image below:

Please note, that you can modify the appearance of visual models using the Inspector.

Protein-Ligand Interaction Analyzer

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. Check out its other tabs for more functionality.

Hydrogen bonds

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.

This will add a new H-bond visual model to the document. If you want to modify the H-bond detection parameters, right-click on the newly created H-bond visual model and choose Inspect from the context menu – this will open the Inspector in which you can modify parameters.

 

That’s all, thank you for completing this tutorial on the Autodock Vina Extended SAMSON Extension. Please do not hesitate to write on our Forum if you have any questions or feedback.

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