Re-scoring Docked Ligands with MM-GBSA

Tutorial Created with Software Release: 2025-3
Topics: Hit Discovery, Small Molecule Drug Discovery, Virtual Screening
Products Used: Glide, Prime

Tutorial files

1.8 MB
This tutorial is written for use with a 3-button mouse with a scroll wheel.
Words found in the Glossary of Terms are shown like this: Workspacethe 3D display area in the center of the main window, where molecular structures are displayed

 

Tip: You can hover over a glossary term to display its definition. You can click on an image to expand it in the page.
Abstract:

 

This tutorial demonstrates how to apply MM-GBSA to re-score the results of a small virtual screen for Factor Xa inhibitors using Glide docking. You will learn how to set up the MM-GBSA calculation and analyze the results in terms of predicted poses and scoring.

Tutorial Content

  1. Introduction to MM-GBSA

  1. Creating Projects and Importing Structures

  1. Setting up the MM-GBSA Calculation

  1. Analyzing the Results of the MM-GBSA Calculation

  1. Conclusion and References

  1. Glossary of Terms

1. Introduction to MM-GBSA

The molecular mechanics with generalized Born and surface area (MM-GBSA) method can be used to approximate the free energy of binding between a protein and a ligand. It uses an implicit solvent model to capture the effect of desolvating ligand and receptor.

There are multiple variants of the method, e.g. using individual energy-minimized structures or ensembles sampled from MD simulations. Within the Schrödinger suite, a Prime MM-GBSA calculation consists of several separate energy calculations:

  • Minimized free receptor
  • Minimized free ligand
  • Minimized complex
  • Isolated energy contributions of ligand and receptor from the minimized complex

The MM-GBSA free energy of binding is therefore calculated as:

Each energy contribution is calculated by using the energies from the force field and an implicit solvation model. The MM-GBSA energy therefore includes ligand and receptor strain energies but neglects all entropic contributions. For more details on the MM-GBSA implementation in the Schrödinger suite and the calculated energy terms, see this knowledge base article.

In cases where the enthalpy dominates the free energy term, MM-GBSA energies can correlate well with experimental binding affinities, especially for congeneric series (although the absolute values are shifted). However, entropic effects play an important role in many ligand-receptor interactions and must be captured by normal mode analysis or molecular dynamics based methods such as free energy perturbation (FEP). MM-GBSA energies should therefore not be used as a direct proxy for the free energy of binding without thorough validation.

MM-GBSA energies are well-suited as a scoring function to rank-order compounds in a virtual screen. Due to its increased computational cost, MM-GBSA is frequently used as the subsequent filtering step on ligand poses obtained from Glide docking.

In this tutorial, you will apply MM-GBSA re-scoring to the Factor Xa ligand set used in the Structure-based virtual screening using Glide tutorial and analyze the results to see if you could improve enrichment.

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location where files are saved in Maestro to make file navigation easier. Each session in Maestro begins with a default Scratch Projecta temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project, which is not saved. A Maestro project stores all your data and has a .prj extension. A project may contain numerous entries corresponding to imported structures, as well as the output of modeling-related tasks. Once a project is saved, the project is automatically saved each time a change is made.

Structures can be built in Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data. The Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion is located to the left of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data can be accessed by Ctrl+T (Cmd+T) or Window > Project Table if you would like to see an expanded view of your project data.

  1. Double-click the Maestro icon.

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory.
  2. Find your directory, and click Choose.
  3. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/mmgbsa_rescore.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location where files are saved for ease of access throughout the tutorial.

Figure 2-2. Saving the project in the Save Project panel.

  1. Go to File > Save Project As.
  2. Change the File name to MMGBSA_rescore_tutorial.
  3. Click Save.
    • The project is now named MMGBSA_rescore_tutorial.prj.

Figure 2-3. The Import panel with desired file selected from the tutorial archive.

  1. Go to File > Import Structures.
  2. Navigate to and select glide_1FJS_screening_pv.maegz in your Working Directorythe location where files are saved.
  3. Click Open.
    • A banner appears confirming the successful import of the Pose Viewer file.
    • A new group glide_1FJS_screening_pv is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

3. Setting up the MM-GBSA Calculation

In this section, you will load in the results of the Glide docking and set up the MM-GBSA calculation for the system. In the Structure-based virtual screening using Glide tutorial, we performed a small virtual screen on a set of potential ligands for Factor Xa obtained from the DUD-E dataset for that target. Glide was able to distinguish between binders and non-binders and enrich the binders in the top scoring compounds. However, Glide returned quite low scores for some of the known binders in the data set. We will now use MM-GBSA to re-score the docked compounds from the screen.

Figure 3-1. Visualizing the docked poses for the ligand set.

First, we’ll have a look at the results from the previous screening stage using Glide docking with a hydrogen bond constraint.

 

  1. Double-click the In circle of 1fjs_prepared in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to fix the receptor structure in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the glide_1FJS_screening_pv group by clicking on the group heading.
  3. Use the left and right arrow keys to step through the ligand poses.

The known actives can be recognized by their CHEMBL IDs. All four known actives originally included in the screening library have docked, albeit partly with low docking scores. See the Structure-based virtual screening using Glide tutorial for a detailed discussion on the results of this screening stage.

Figure 3-2. The Structures section of the Prime MM-GBSA panel.

Using MM-GBSA, you will now refine the scoring with the goal of further enriching the known actives in the top-scoring compounds.

 

  1. Go to Tasks > Browse > Prime > MM-GBSA.
    • The Prime MM-GBSA panel opens.
  2. Under Structures, choose Take complexes from a Maestro Pose Viewer file.
  3. Click Browse, and select glide_1FJS_screening_pv.maegz.
  4. Click Open.

For this calculation, we use the VSGB water model to simulate solvation which is essential for accurately capturing protein-ligand binding. If your target is a membrane protein, you should set up an implicit membrane using the Prime Membrane Setup panel and choose “Use implicit membrane” in the Options section of the MM-GBSA panel.

The options in the Protein flexibility section allow you to choose whether to make parts of the protein flexible. By default, only the ligand atoms are moveable in the optimization of the protein-ligand complex. The more flexible residues are added, the larger the computational cost of the calculation.

Note that regardless of how much of the protein you allow to relax, energy minimization can not fully capture large-scale conformational changes. The optimal induced-fit protein-ligand geometry may be outside the local minimum the optimization algorithm converges to. For a proper modeling of induced-fit effects, use IFD-MD.

Figure 3-3. Running the Prime MM-GBSA job.

  1. Change the Job name to prime_mmgbsa_FXa_rigid
  2. Click Run.
    • This job takes approximately 40 minutes to run on one CPU core.
    • The results are automatically incorporated into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Note: If you want to skip running the calculation yourself, you can see the pre-generated results by importing the prime_mmgbsa_FXa_rigid-out.maegz file from the tutorial archive.

 

  1. Close the Prime MM-GBSA panel.

4. Analyzing the Results of the MM-GBSA Calculation

In this section, you will analyze the results of the re-scoring of the ligand set with MM-GBSA. Keep in mind that the data set we have here is very small in order to keep the calculations short, and closer to what might be used as a validation set for setting up the screening pipeline. You will compare the ranking obtained from Glide docking with that obtained from MM-GBSA, focusing on two ligands in particular.

Figure 4-1. Selecting the output group and showing the properties.

Before diving into the results, you will add the docking score, MM-GBSA energy and the experimental binding activity to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion so you can see them at a glance.

 

  1. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the prime_mmgbsa_FXa_rigid-out group.
  2. Click the Change table settings (three vertical dots) in the top right corner of the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  3. Choose Show Property.
    • The Show Properties in Table dialog box opens.

 

Figure 4-2. Adding properties for analyzing the result.

  1. In the dialog, click Choose.
  2. Search for and select docking score, MMGBSA dG Bind, and Activity from the list.
  3. Click OK.
    • The selected properties are added to the table.

Note: You may need to drag the border of the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to the right to make the added columns visible.

Both the docking scores and the MM-GBSA energy are defined in such a way as to behave similarly to the free energy of binding: the more negative the number, the stronger the interaction. The experimental activities for the known binders are provided as Ki [nM].

Figure 4-3. Sorting the MM-GBSA results for selected entries.

Now, you will sort the re-scoring results by the MM-GBSA energy.

 

  1. Right-click the MM-GBSA dG Bind column header in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  2. Choose Sort Selected (Ascending)
    • Only the MM-GBSA results are sorted.

By comparing the ranking of the Glide docking (which are still sorted by docking score) and the MM-GBSA calculation, you can see the difference that the re-scoring makes for this (very small) data set. Ranked by MM-GBSA energies, now all but one of the known binders are scored in the top five compounds. Let’s look at the two known binders with bad Glide scores, CHEMBL174558 and CHEMBL280947 in more detail.

Figure 4-4. Comparing poses for CHEMBL174558 obtained from Glide docking (gray carbons) and MM-GBSA (green carbons).

  1. Ctrl+Click (Cmd+Click) to includethe entry is represented in the Workspace, the circle in the In column is blue both the entries for CHEMBL174558.
  2. Turn on interactions from the Interactions Toggle (bottom right corner).
    • CHEMBL174558, which had a middling docking score but which MM-GBSA clearly ranks as a promising binder.

 

Figure 4-5. Comparing poses for CHEMBL280947 obtained from Glide docking (gray carbons) and MM-GBSA (orange carbons).

  1. Right-click the In circle of both the entries for CHEMBL174558 and choose Exclude.
    • The entries are excluded from the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Includethe entry is represented in the Workspace, the circle in the In column is blue both entries for CHEMBL280947.
  3. Repeat the same steps to compare docked and MM-GBSA poses for CHEMBL280947.

For CHEMBL174558, the optimized pose returned by MM-GBSA leads to a much more plausible H-bond network near the guanidino group deep in the pocket, which is reflected in the scoring. In this case, the re-scoring has correctly improved the ranking of the compound and generated a more realistic pose.

 

The MM-GBSA score for CHEMBL280947 is catastrophically bad (MMGBSA dG Bind > 0 means that the complex is unstable). Comparing the poses obtained for this ligand from both methods shows that the substituent on the imidazole ring deep in the pocket clashes with the surrounding residues for both the Glide and MM-GBSA pose. The MM-GBSA refinement doesn’t improve things, and even causes the phenyl linker to distort.

These observations imply that this binding mode is not plausible for this ligand. Looking into the original publication for the ligand series CHEMBL280947 belongs to (see references) shows that the ligand should bind with the naphthyl group in the deep part of the pocket near ASP 189. The bad pose is therefore a result of the hydrogen-bond constraint enforced in the docking protocol. Docking this compound without the constraint recovers the correct pose:

Figure 4-6. Docked poses for CHEMBL280947 with (white) and without (green) enforcing a hydrogen bond to ASP189 (upper left corner).

5. Conclusion and References

In this tutorial, you learned how to use Prime MM-GBSA to re-score the results of a Glide docking stage of a virtual screen to further improve compound ranking, as well as how to analyze the results of this calculation. In the small example data set, MM-GBSA rescoring led to further enrichment of the known active compounds in the top ranked results, further refined the ligand poses, and flagged a bad pose resulting from constraints used in the docking calculations.

When applying Prime MM-GBSA to your own virtual screening project, keep in mind that the method uses an implicit solvation model and does not consider entropic contributions to protein-ligand binding. The MM-GBSA energies should therefore not be expected to correlate with experimental binding affinities for a given protein-ligand system without thorough validation. Rather, the usefulness of MM-GBSA calculations is as a pre-filter that is more accurate than Glide docking, and the ability to optimize poses that can then be used in FEP calculations.

For further reading:

6. Glossary of Terms

Entries - a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion

Included - the entry is represented in the Workspace, the circle in the In column is blue

Project Table - displays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data

Recent actions - This is a list of your recent actions, which you can use to reopen a panel, displayed below the Browse row. (Right-click to delete.)

Scratch Project - a temporary project in which work is not saved, closing a scratch project removes all current work and begins a new scratch project

Selected - (1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries

Working Directory - the location where files are saved

Workspace - the 3D display area in the center of the main window, where molecular structures are displayed