Modeling Receptor Binding in an Olfactory Protein

Tutorial Created with Software Release: 2025-2
Topics: Consumer Packaged Goods, Hit Discovery, Structure Prediction & Target Enablement
Products Used: Glide, MS Maestro

Tutorial files

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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:

 

In this tutorial, we will learn how to prepare structures for docking and create a protein mutation by modeling an olfactory receptor.

 

Tutorial Content

  1. Introduction to Odorant Receptors

  1. Creating Projects and Importing Structures

  1. Protein Structure Preparation

  1. Ligand Preparation

  2. Docking
  3. Protein Mutant Creation
  4. Mutated Protein Docking
  5. Conclusion and References

  1. Glossary of Terms

1. Introduction to Odorant Receptors

Olfactory proteins are G protein-coupled receptors (GPCR) that can bind odorants in their binding pocket. Olfactory proteins are responsible for our sense of smell. Billesbølle et al. (see References) have crystallized the human olfactory receptor 8F76 with fatty acid propionate bound in the pocket. Cryo-electron microscopy has determined that propionate interacts with specific active site residues that play an important part in receptor activation. The authors speculate that the selectivity of the protein for propionate arises from the small volume of the binding pocket. They show that in order for the odorant-binding pocket to bind with larger fatty acids, binding site mutations need to be created to widen the pocket. By creating two mutations Billesbølle et al have widened the binding site by 200% and 300%, respectively, allowing larger fatty acids to bind. Ultimately suggesting that odorant selectivity is controlled by the binding site interactions.

In this tutorial, we will use several panels in the Materials Science (MS) Maestro interface to perform a variety of calculations for studying protein/ligand interactions to reproduce the findings from Billesbølle et al.

First, we will begin by using the Protein Preparation Workflow panel to prepare an olfactory protein structure and the LigPrep panel to prepare three different fatty acids. Second, using the prepared output structures, we will use the Receptor Grid Generation and Ligand Docking panels to dock the different fatty acids and view the binding site interactions.

The first workflow is summarized in the following schematic:

In this particular case, docking fatty acids longer than the ones in the protein’s crystal structure results in numerous negative interactions and clashes in the binding site. Using the Residue Scanning panel, we will create two mutations to make the binding site wider by about 200% and 300%, respectively. The expanded binding sites can easily accommodate our larger fatty acids of interest. By redocking these larger fatty acids into the mutated proteins, we observe a significant reduction in negative clashes.

The second workflow is summarized in the following schematic:

Specifically, we will prepare the protein 8F76, a human olfactory receptor bound to propionate, and three fatty acids (propionate, hexanoate, and octanoate). Numerous clashes between 8F76 and hexanoate and octanoate are expected within the binding site. Introducing two distinct protein mutations (L158A and F155A) will widen the binding site and effectively diminish these clashes within the pocket.

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 MS Maestro to make file navigation easier. Each session in MS 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 MS 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 MS Maestro or can be imported using File > Import Structures (or drag-and-dropped), and are added to the Entry Lista 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 Entry Lista 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.

OR

  1. Double click the Maestro or Materials Science icon to start Maestro or MS Maestro
    • (No icon? See Starting Maestro)
    • This tutorial uses MS Maestro, but this workflow can be performed in Maestro or MS Maestro. Use whichever interface you are comfortable with or typically use for your projects.

 

Note: Specific licenses are needed to run this tutorial beyond the typical MS licenses.

Figure 2-1. Change Working Directory option.

  1. Go to File > Change Working Directory
  2. Find your directory, and click Choose
  3. Pre-generated files are included for running jobs or examining output. Download the zip file here: schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/olfactory_receptor_binding.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. Save Project panel.

  1. Go to File > Save Project As
  2. Change the File name to receptor_binding_tutorial, click Save
    • The project is now named receptor_binding_tutorial.prj

3. Protein Structure Preparation

Structure files obtained from the Protein Data Bank (PDB), vendors, and other sources often lack necessary information for performing modeling-related tasks. Typically, these files are missing hydrogens, partial charges, side chains, and/or whole loop regions. Proteins in their raw state may also have incorrect bond order assignments and group orientations. To make these structures suitable for modeling tasks, we will use the Protein Preparation Workflow panel to resolve common structural issues.

Figure 3-1. The Protein Preparation Workflow panel.

Let’s start by importing and preparing the protein of interest.

  1. Go to Tasks > Browse All > Protein Preparation and Refinement > Protein Preparation Workflow
  2. Click Get PBD

Figure 3-2. Importing the 8F76 PDB file.

  1. For PDB IDs, type 8F76
    • 8F76 is a human olfactory receptor bound to propionate
  2. Click Download

Figure 3-3. The 8F76 PDB structure.

The PDB structure 8F76 has been loaded into the workspacethe 3D display area in the center of the main window, where molecular structures are displayed

Figure 3-4. Switching to the interactive mode in the Protein Preparation Workflow panel.

  1. Back in the Protein Preparation Workflow, click INTERACTIVE
    • Preparing the protein in interactive mode allows us to prepare the protein in a step-by-step manner with the opportunity to review the results at each step and make decisions about how to address any problems.
    • However, if we wanted to prepare many proteins at once we would not want to use interactive mode as each issue would still need to be addressed individually for each protein.

Figure 3-5. Step 2 of the Protein Preparation Workflow.

  1. Click Preprocess
    • This step preprocesses the protein by fixing structural defects and performs a refinement job to place and optimize the missing side chains, if any.

Figure 3-6. Step 3 of the Protein Preparation Workflow.

A new structure has appeared in the entry list a simplified view of the Project Table that allows you to perform basic operations such as selection and inclusiontitled 8F76 - 2-preprocessed, and is automatically 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and includedthe entry is represented in the Workspace, the circle in the In column is blue in the workspace.

 

  1. In the Diagnose and Analyze section of the Protein Preparation Workflow panel click Check Structure
    • This step diagnoses structural issues and analyzes the substructures.

Figure 3-7. Removing some chains.

8F76 is composed of 5 different chains. The binding pocket is in chain A so we can delete the other 4 chains.

  1. Select Chains N, X, Y, Z and click Delete from Entry

Figure 3-8. Editing the protein substructure.

A new structure has appeared in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled 8F76 - 3-substructures-deleted, and is automatically 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and Includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

  1. In the Protein Preparation Workflow panel click Workflow to return back to the main Protein Preparation Workflow

Figure 3-9. Step 4 of the Protein Preparation Workflow.

  1. In the Optimize H-bond Assignments section of the panel, click Optimize
    • This step optimizes the hydrogen bonding network within the structure

Figure 3-10. Step 5 of the Protein Preparation Workflow.

A new structure has appeared in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled 8F76 - 4-hbond-opt, and is automatically 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and Includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

  1. In the Minimize and Delete Waters section of the Protein Preparation Workflow panel, click Clean Up to perform a minimization and remove the water molecules
  2. Close the Protein Preparation Workflow panel

Figure 3-11. Fully prepared 8F76.

A new structure has appeared in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion titled 8F76 - 5-removed waters, and is automatically 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries and Includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. This structure is the fully prepared protein structure.

Feel free to visualize the structure in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

4. Ligand Preparation

In this section, we will use the LigPrep panel to rapidly prepare three fatty acids for docking that will be performed in Section 5.

Figure 4-1. The three fatty acids after importing.

Let’s start off by importing our three fatty acids. These could also be drawn using the 2D or 3D sketching tools in MS Maestro. For a complete overview of using the sketcher panel, see the 2D Sketcher Panel documentation or watch the Building Small Molecules video in the Getting Going with Materials Science Maestro Video Series.

  1. Go to File > Import Structures
  2. Navigate to where you downloaded the provided tutorial files, choose ligands.maegz and click Open
    • A new group appears in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion called ligands that is composed of three individual fatty acids
  3. 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries all three fatty acids

Figure 4-2. LigPrep panel.

  1. To prepare the fatty acids, go to Tasks > Browse All > LigPrep

Figure 4-3. Running the LigPrep panel.

  1. Ensure that Use structures from shows Project Table (3 selected)
  2. Check the Determine chiralities from 3D structure box
    • While this option does not impact our fatty acids of interest, it is recommended to check the box for best practices when working with 3D molecules that have a specified stereochemistry that you want to preserve.
  3. Change the Job Name to ligprep_ligands
  4. Adjust the job settings () as needed and click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 4-4. LigPrep output.

When the calculation is finished, the three prepared fatty acids will appear in the Entry List. Feel free to adjust the style or color of the fatty acids. In this Figure, thin tube representation has been applied and H atoms have been hidden.

5. Docking

In this section, we will dock the three prepared fatty acids to the binding site of 8F76 using the Receptor Grid Generation panel and the Ligand Docking panel. We will then view the interactions between the three fatty acids and the binding site of 8F76.

Figure 5-1. Open the Receptor Grid Generation panel.

Before the three fatty acids can be docked into 8F76, we need to generate a grid of the binding site.

  1. With 8F76 - 5-removed waters includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Browse All > Glide > Receptor Grid Generation

Figure 5-2. Select the ligand.

  1. Select the ligand (fatty acid) in the binding site of 8F76 and double click
    • The ligand can be selected in many different ways. One way is to select the ligand from the Quick Select menu then change the fit to view the selected atoms.
    • A green X, Y, Z axes will appear when selected.
    • We want to identify the fatty acid so it can be excluded from the grid generation.

Figure 5-3. Run the calculation to determine the grid.

  1. Change the Job Name to glide-grid_8F76
  2. Adjust the job settings () as needed and click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

 

When the grid is calculated a new structure will not appear in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. Instead a zip file is created that we will use in the next step.

Figure 5-4. Open the Ligand Docking panel.

  1. To open the Ligand Docking panel, go to Tasks > Browse All > Glide > Ligand Docking
  2. Click Browse…
    • Navigate to the job directory for glide-grid_8F76

Figure 5-5. Select the zip file from the grid generation calculation.

  1. Select glide-grid_8F76.zip and click Open

Figure 5-6. Setting up and running the docking calculation.

The zip file will now be included in the Ligand Docking panel

  1. Select the three fatty acids from the ligprep output in your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  2. Select Project Table (3 selected) from the Use ligands from menu
  3. Change the Job Name to glide-dock_8F76
  4. Adjust the job settings () as needed
  5. Click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 5-7. The docking results.

When the job has completed, a new group will appear in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion. This group will contain four entries, 8F76 and the three fatty acids.

To view the docked fatty acid, both the protein and fatty acid of interest need to be Includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 5-8. Propionate docked in the binding site of 8F76.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue both 8F76 - 5-removed waters and propionate
    • Zoom in on the fatty acid
    • Feel free to stylize as you wish
  2. Turn on the Interactions Toggle in the bottom right corner to view the clashes between the fatty acid and protein
    • The three dots above the Interactions Toggle button shows a key for all the different dashed line colors
    • Orange and red dashed lines signify bad and ugly interactions, we want to minimize these two unfavorable interactions

 

 

Figure 5-9. Hexanoate docked in the binding site of 8F76.

Next, let’s look at the interactions with hexanoate.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue both 8F76 - 5-removed waters and hexanoate
    • Zoom in on the fatty acid again.
    • The interactions toggle should still be turned on.
    • Now we see a lot more orange and red dashed lines that signify unfavorable interactions.

Figure 5-10. Octanoate docked in the binding site of 8F76.

Lastly, let’s look at the interactions and clashes between octanoate and 8F76.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue both 8F76 - 5-removed waters and octanoate
    • Zoom in on the fatty acid again.
    • The interactions toggle should still be turned on.
    • Once again, there are a lot more orange and red dashed lines that signify unfavorable interactions.

 

We do not want these unfavorable interactions between the fatty acid and 8F76 so to minimize these interactions let’s mutate a residue in the binding site of 8F76 to widen the binding pocket.

6. Protein Mutant Creation

As we saw in Section 5, there were several clashes in the binding pocket between the larger fatty acids and 8F76. In this section, we will create two protein mutants (L158A and F155A) which will widen the binding pocket by about 200% and 300%, respectively. Creating this wider pocket will allow our larger fatty acids to successfully bind with fewer clashes, which we will explore in Section 7.

Figure 6-1. Select the original prepared 8F76 structure.

To create a mutation in the protein structure, let’s return to the original 8F76 prepared structure.

  1. With 8F76 - 5-removed waters Includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Browse All > Biologics > MM-GBSA Residue Scanning Calculations

Figure 6-2. The Residue Scanning panel.

  1. From the Import structures from dropdown select Workspace and then click Import

Figure 6-3. Mutating residue 158.

The residues from the 8F76 protein have been imported into the panel. We want to mutate residue 158 from leucine to alanine.

  1. Scroll down to residue 158 and click None (click to add)
  2. Select ALA
    • Ala is the three letter code for alanine
  3. Close the pop-up dialog box

Figure 6-4. Generating L158A.

  1. Change the Job Name to mmgbsa_residue_scanning_L158A
  2. Adjust the job settings () as needed
  3. Click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 6-5. The Residue Scanning Viewer panel.

When the mutant has been created, the MM-GBSA Residue Scanning Viewer panel will appear. This panel displays the residues that were mutated. You can examine changes in various properties, both in a table and graph format. Feel free to explore this panel and close once finished.

Figure 6-6. Generate mutant F155A.

We want to create a second mutant structure by mutating residue 155 from phenylalanine to alanine.

  1. Once again with 8F76 - 5-removed waters includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Browse All > Biologics > Residue Scanning Calculations
  2. Follow steps 2-5 in this section to create mutant F155A
  3. Change the Job Name to mmgbsa_residue_scanning_F155A
  4. Adjust the job settings () as needed
  5. Click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.
    • Close the Residue Scanning Viewer panel when the calculation completes.

 

Two different mutants have been created, L158A and F155A

7. Mutated Protein Docking

In this section, we will dock hexanoate into L158A and octanoate into F155A. We will then compare the clashes in the binding pocket between the mutants and the wildtype protein.

Figure 7-1. Preparing the receptor grid for L158A.

Following the steps from Section 5, let’s first dock hexanoate into L158A.

  1. With 8F76 - 5-removed waters_Mutant_A:158 ALA Includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Browse All > Glide > Receptor Grid Generation
  2. Select the ligand in the binding site of L158A by double clicking the ligand
    • A green X, Y, Z axes will appear when selected
  3. Change the Job Name to glide-grid_L158A
  4. Adjust the job settings () as needed and click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 7-2. Docking hexanoate into L158A.

Next, let’s dock hexanoate into L158A

  1. To open the Ligand Docking panel, go to Tasks > Browse All > Glide > Ligand Docking
  2. Click Browse…
    • Navigate to the job directory for glide-grid_L158A
  3. Select glide-grid_L158A.zip and click Open
    • The zip file will now be included in the Ligand Docking panel.
  4. Select the hexanoate ligand from the ligprep output in your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  5. Select Project Table (1 selected) from the Use ligands from menu
  6. Change the Job Name to glide-dock_L158A_hexanoate
  7. Adjust the job settings () as needed
  8. Click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 7-3. Viewing the interactions between hexanoate and L158A.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue both 8F76 - 5-removed waters_Mutant_A:158 ALA and hexanoate
    • Zoom in on the ligand
    • Feel free to stylize as you wish
    • In the Figure, H atoms are hidden to better show the ligand
  2. Turn on the Interactions Toggle in the bottom right corner to view the clashes between the ligand and protein
    • Now we see only 1 unfavorable interaction between the ligand and L158A

 

Creating the L158A mutation has widened the binding pocket by about 200% which significantly decreases the clashes in the binding pocket when hexanoate is docked.

Figure 7-4. Preparing the receptor grid for F155A.

Using these same steps, let’s next dock octanoate into F155A.

  1. With 8F76 - 5-removed waters_Mutant_A:155 ALA includedthe entry is represented in the Workspace, the circle in the In column is blue and 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, go to Tasks > Browse All > Glide > Receptor Grid Generation
  2. Select the ligand in the binding site of F155A by double clicking the ligand
    • A green X, Y, Z axes will appear when selected
  3. Change the Job Name to glide-grid_F155A
  4. Adjust the job settings () as needed and click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 7-5. Docking octanoate onto F155A.

Next, let’s dock octanoate into F155A

  1. To open the Ligand Docking panel, go to Tasks > Browse All > Glide > Ligand Docking
  2. Click Browse
    • Navigate to the job directory for glide-grid_F155A
  3. Select glide-grid_F155A.zip and click Open
    • The zip file will now be included in the Ligand Docking panel
  4. Select the octanoate ligand from the ligprep output in your entry lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion
  5. Select Project Table (1 selected) from the Use ligands from menu
  6. Change the Job Name to glide-dock_F155A_octanoate
  7. Adjust the job settings () as needed
  8. Click Run
    • This job requires a CPU host. The job can be completed in a couple minutes using 1 CPU.

Figure 7-6. Viewing the interactions between octanoate and F155A.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue both 8F76 - 5-removed waters_Mutant_A:155 ALA and octanoate
    • Zoom in on the ligand
    • Feel free to stylize as you wish
  2. Turn on the Interactions Toggle in the bottom right corner to view the clashes between the ligand and protein
    • We do not see any unfavorable interactions between the ligand and F155A

 

Creating the mutation has widened the binding pocket by about 300% and removed all the clashes.

To summarize the receptor binding between the wildtype and mutated protein, shown below are side by side comparisons of hexanoate docked into the pocket of 8F76 (left) and L158A (right). The number of unfavorable clashes has significantly reduced in the mutant structure.

 

 

As well as, side by side comparisons of octanoate docked into the pocket of 8F76 (left) and F155A (right). Once again, the number of unfavorable clashes has significantly reduced in the mutant structure.

 

8. Conclusion and References

In this tutorial, we learned how to prepare a protein and ligand, create a protein mutation, and dock the ligand into the protein’s binding site to examine the binding interactions.

For further learning:

For introductory content, focused on navigating the Schrödinger Materials Science interface, an Introduction to Materials Science Maestro tutorial is available. Please visit the materials science training website for access to 70+ tutorials. For scientific inquiries or technical troubleshooting, submit a ticket to our Technical Support Scientists at help@schrodinger.com.

For self-paced, asynchronous, online courses in Materials Science modeling, including access to Schrödinger software, please visit the Schrödinger Online Learning portal on our website.

For some related practice, proceed to explore other relevant tutorials:

For further reading:

9. Glossary of Terms

Entry List - 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 Entry List (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