Covalent Docking for Virtual Screening and Pose Prediction

Tutorial Created with Software Release: 2025-3
Topics: Hit Discovery, Hit-to-Lead & Lead Optimization, Ligand Preparations and Library Design, Virtual Screening
Products Used: Glide, Prime

Tutorial files

47.7 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:

 

In this tutorial, you will create and validate a covalent docking model for human cathepsin L (hCatL), a cysteine protease forming a covalent thioimidate adduct with an activated nitrile group. You will learn how to enumerate a provided ligand scaffold into the S2 pocket to create a diverse ligand set for docking investigations. This system, and enumerated ligands will then be used to perform covalent docking virtual screening using a predefined chemistry pattern available in the interface.

 

Tutorial Content

  1. What is Covalent Docking?

  1. Creating Projects and Importing Structures

  1. Protein Preparation and Ligand Enumeration

  1. Validating the Covalent Docking Protocol Using the Cocrystal Ligand

  1. Covalently Docking an Enumerated Series into the Protein

  1. Conclusion and References

  1. Glossary of Terms

1. What is Covalent Docking?

Distinct from the conventional design of small molecules, covalent inhibition works through forming an explicit bond to the target which can be either reversible or irreversible. Concepts such as how long the bond forms, the percentage occupancy in the active site, and specificity or off-target binding are a few of the many important factors to be considered in the design of these molecules.

Well known examples of covalent inhibitors include aspirin (marketed over 100 years ago), penicillin (discovered in 1928), and omeprazole (a blockbuster proton pump inhibitor).  While they contribute to a wide range of therapeutic areas such as infectious diseases, cancer treatment, and gastrointestinal disorders, they are particularly useful for long-term therapies such as those used in CNS disorders, e.g. Parkinson's disease, due to the very nature of covalent bond formation. Covalent inhibitors make up a respectable 30% of marketed drugs to date (see this publication).

Sotorasib is an example of a covalently bound inhibitor that has recently met FDA approval. It is a once-daily oral treatment for people living with non-small cell lung cancer (NSCLC) whose tumor is KRAS(G12C) positive. The mutant cysteine of KRAS(G12C) resides adjacent to a pocket (P2) that is present in the inactive GDP-bound form of KRAS. Activating mutations in KRAS prevent the association of GTPase-activating proteins, thus stabilizing effector binding and enhancing KRAS signaling. Sotorasib inhibits this process by forming a covalent bond with the cysteine mutant of KRAS(G12C) and is able to shrink and/or suppress tumor growth in patients.

Canon, J., Rex, K., Saiki, A.Y. et al. The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity. Nature 575, 217–223 (2019)

Figure 1-1: Sotorasib forming a covalent bond with the cysteine mutant of KRAS(G12C) (PDB ID: 6OIM).

2. Creating Projects and Importing Structures

At the start of the session, change the file path to your chosen Working Directorythe location that 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 created, the project is automatically saved each time a change is made.

Structures can be imported from the PDB directly, or from your Working Directorythe location that files are saved using File > Import Structures, 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 to start Maestro.

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/covdock.zip
  4. After downloading the zip file, unzip the contents in your Working Directorythe location that files are saved for ease of access throughout the tutorial.

Figure 2-2. The Open Project Panel.

  1. Go to File > Open Project.
  2. Select CovDock_tutorial.prjzip and click Open.
    • The structures are added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
    • 5MQY is 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.
  3. In the Save scratch project dialog box, click OK.

 

Note: For the difference between 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 Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries , please refer to the Glossary of Terms.

Figure 2-3. Saving the project in the Save Project Panel.

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

3. Protein Preparation and Ligand Enumeration

Structure files obtained from the 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. In order to make these structures suitable for modeling tasks, we use the Protein Preparation Workflow to resolve these issues. Similarly, ligand files can be sourced from numerous places, such as vendors or databases, often in the form of 1D or 2D structures with unstandardized chemistry. In this tutorial, a premade R-group library has been provided  for enumeration of a template scaffold in the S2 binding pocket. This site was chosen because SAR knowledge in the S2 pocket is very limited for this scaffold and it is amenable to diverse chemical modifications. If you would like to learn more, the structures from this tutorial, as well as the enumeration investigation of the S2 pocket originated from the publication: “Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors” (J. Med. Chem. 2017, 60(6): 2485-2497). After enumeration, LigPrep can convert ligand files to 3D structures, with the chemistry properly standardized and extrapolated, ready for use in virtual screening. Ligands to be used for covalent docking must first be prepared using LigPrep.

In this tutorial, 5MQY protein structure has already been prepared and included in the tutorial files in order to save time. During preparation, crystallographic artifacts were removed, "Cap termini" and "Fill in missing loops (Using Prime)" were checked under Preprocess. Default settings were used for all other steps. The ligand structures have also been prepared using LigPrep. These preparation steps are a necessary part of covalent docking. Please see the Introduction to Structure Preparation and Visualization tutorial for instructions on using the Protein Preparation Workflow and LigPrep.

Figure 3-1. Opening the Ligand Interaction Diagram.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue and 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   5MQY – prepared.

 

The 2D Ligand Interaction diagram will help you visualize the covalent thioimidate adduct with the catalytic CYS 25 residue.

 

  1. Go to Tasks > Structure Analysis > Ligand Interaction Diagram.

Figure 3-2. The Ligand Interaction Diagram depicting binding pockets and covalent C-S bond.

Note: In this tutorial, you will focus on the S2 pocket for enumeration.

 

  1. Close the Ligand Interaction Diagram.

Figure 3-3. Visualizing the interaction between CYS 25 residue and the ligand.

  1. Double-click Presets.
    • The default Custom Preset is applied to the structure.
    • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed zooms to the ligand.
  2. Turn-on the Interactions Toggle (bottom right corner).
    • The ligand-receptor interactions are shown as colored dashed lines in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • Rotate the structure and try visualizing the interaction between CYS 25 residue and the ligand.

 

 

Differentiating the protein from the ligand in covalent complexes can be challenging. Sometimes, it may be necessary to break bonds and/or rename the species prior to docking. For this tutorial, renaming was not required as an independent ligand file was used. To rename the ligand, go to Build > Other Edits > Change Atom Properties > Residue Name.

Figure 3-4. Splitting the prepared structure into Ligands, Water, Other.

  1. Right click 5MQY – prepared.
  2. Choose Split > Into Ligands, Water, Other.
    • A new group with three entries is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

 

Figure 3-5. Tiling the ligands in the Workspace.

 

  1. Ctrl+Click (Cmd+Click) to includethe entry is represented in the Workspace, the circle in the In column is blue 5MQY – prepared_ligand and 5MQY – prepared_ligand_modified in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Note: 5MQY – prepared_ligand_modified is the ligand isolated from the 5MQY crystal structure. It has been prepared using the LigPrep panel at pH 7.4. The alkene has been modified to an alkyne to prepare for covalent docking using the appropriate reaction. This is done to prepare the ligand for pose prediction docking. This crystal ligand will be used to test the model. This step is not required for Covalent Docking receptor grid generation.

 

See Preparing Structures for Covalent Docking for more information.

 

  1. Click the Show Workspace Configuration panel icon (plus symbol at the bottom right corner).
  2. Choose Tile.
    • The structures are tiled in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 3-6. The Ligand Alignment in Tasks.

  1. Go to Tasks > Structure Alignment > Ligand Alignment.
    • The Ligand Alignment panel opens.

Figure 3-7. Running the Ligand Alignment job.

  1. For Align ligands from, choose Workspace (2 included entries).
  2. For Reference, choose User-specified.
  3. Choose the reference as 3:5MQY – prepared_ligand.
  4. Check the box for Overwrite existing entries.
  5. Change the Job name to align_ligands_5MQY.
  6. Click Run.
    • This job takes a few seconds.
  7. Close the Ligand Alignment panel.
  8. In the Workspace configuration panel, click Tile by to un-tile the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

4. Validating the Covalent Docking Protocol Using the Cocrystal Ligand

This section demonstrates how to set up a covalent docking job in virtual screening and pose prediction modes. The system chosen is a crystal structure of human cathepsin L (hCatL), a cysteine protease complexed with an inhibitor, (PDB ID: 5MQY) and this inhibitor is self-docked to the receptor by means of a covalent thioimidate adduct bond formation with the activated nitrile group.

Virtual Screening mode provides a fast and accurate way to predict poses for covalent protein-ligand complexes, while Pose Prediction mode is a more thorough method of performing covalent docking calculations. In this tutorial, Pose Prediction mode will be used to compare the docking model’s result with the docked ligand in the original crystal structure.

4.1 Covalent docking in pose prediction mode

Figure 4-1. The Covalent Docking in Tasks.

You will now set up the Pose Prediction docking job using the Covalent Docking panel.

 

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue 5MQY – prepared 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 5MQY_prepared_ligand_modified in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

 

Note: Any ligand could be selected here, but this pose prediction calculation is intended to test the model and compare the results with that of the initial crystal structure.

 

  1. Go to Tasks > Browse > Glide > Covalent Docking.
    • The Covalent Docking panel opens in the Receptor tab.

Figure 4-2. The Receptor tab of the Covalent Docking Panel.

  1. Under Use ligands from, choose Project Table (1 selected entry).
  2. Under Reactive Residue, check the box for Pick and click on the CYS 25 residue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • The field for the reactive residue is updated in the panel to read A:25.
  3. Under Centroid of Workspace ligand check the box for Pick and select the ligand in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • The field is updated with A:301.

 

Note: The Centroid of Workspace option uses the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed ligand to define the centroid of the active site for docking.

Figure 4-3. Receptor grid generation view in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: Your Workspacethe 3D display area in the center of the main window, where molecular structures are displayed should look like this. The CYS 25 residue is highlighted. The ribbons are hidden ribbons to declutter the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 4-4. Specifying the Reaction Type in the Covalent Docking panel.

  1. Go to the Reaction Type tab.
  2. For Reaction Type, choose Nucleophilic Addition to a Triple Bond.

 

Note: For Reaction types not available in this option list, see the custom reaction repository here: CovDock.

 

Figure 4-5. Forming the covalent thioimidate adduct.

Note: This is an example of a similar ligand complex forming the same covalent thioimidate adduct with the Cys 25 residue. This will be the template backbone structure later used for virtual screening, altering the substituent in the S2 pocket.

ChemMedChem 2013, 8, 967 – 975

Figure 4-6. Running the Covalent Docking job in Pose Prediction mode.

  1. Go to the Docking tab.
  2. For the Docking Mode select Pose Prediction (Thorough).
  3. Set Output poses per ligand reaction site to 1.
  4. Change Job name to 5MQY_pose_prediction.
  5. Click Run.
    • This job takes ~20 minutes.
    • To save time, you may import the pre-generated results by going to  File > Import Structures and select 5MQY_pose_prediction-out.maegz from the 5MQY_pose_prediction folder in your Working Directorythe location that files are saved.
  6. Close the Covalent Docking panel.

4.2 Analyze the results from pose prediction covalent docking

Figure 4-7. A view of the CYS 25 crystal structure pose (gray) and the best Prime predicted CovDock pose (green), included in the Workspace. The covalent bond to CYS 25 is shown in the orange box.

  1. Ctrl+Click (Cmd+Click) to includethe entry is represented in the Workspace, the circle in the In column is blue 5MQY – prepared and 5MQY – prepared_ligand_modified from the 5MQY_pose_prediction-out group.

 

Note: If you had chosen to generate more poses, they would all be present in this group and ranked according to their Prime Energies.

 

  1. Double-click Presets.
    • Confirm the covalent bond present in your pose result aligns well with the prepared original cognate ligand.

Figure 4-8. The Show Property option.

  1. Click the Change table settings icon (three vertical dots) and choose Show property.
    • The Show Properties in Table dialog box opens.

Figure 4-9. Adding the properties to the Entries table.

  1. Search and select cdock affinity and score docking score from the list.
  2. Click OK.
    • The selected properties are added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion table.
    • You may need to click and drag the edge of the table towards the right to see the added properties.

Figure 4-10. The updated Entries table showing the added properties.

Note: See here for more information about the properties associated with Covalent Docking outputs.

5. Covalently Docking an Enumerated Series into the Protein

5.1 Enumerate the S2 pocket

Figure: 5-1. Selecting the R-group for enumeration.

You will now set up the Virtual Screening docking job using the Covalent Docking panel.

 

  1. Go to File > Import Structures.
  2. Navigate to and select Template_scaffold.mae in your Working Directorythe location that files are saved.
  3. Includethe entry is represented in the Workspace, the circle in the In column is blue and 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 Template_Scaffold in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  4. 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 carbon adjacent to the nitrogen in the S2 pocket.

Figure 5-2. The R-Group Enumeration option in Enumeration and Ideation in Tasks.

  1. Go to Tasks > Browse > Enumeration and Ideation > R-Group Enumeration.
    • The Custom R-Group Enumeration panel opens.

This tutorial uses a pre-generated ligand library, however, you can import any fragment library from a file or generate one using the R-Group Creator panel. Additionally, Maestro includes several pre-packaged libraries. For more information about ligand enumeration, please refer to the Enumeration Tools for Library Design tutorial.

Figure 5-3. The Custom R-Group Enumeration panel.

  1. For R-Group Library, choose File.
    • A dialog box opens to select a collection fragment file to use.

Figure 5-4. Loading the pre-generated R-group library.

  1. Navigate to and select CovDock_Tutorial_Ligands_for_S2_Pocket.mae from the S2_pocket_enumeration folder in your Working Directorythe location that files are saved.
  2. Click Open.
    • The R-Group Library column gets updated.

Figure 5-5. Running the enumeration job.

  1. Change the Job name to S2_pocket_enumeration.
  2. Click Run.
    • This job takes a few seconds.
    • A new group S2_pocket_enumeration with 35 ligands is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  3. Close the Custom R-Group Enumeration panel.

Figure 5-6. Opening the LigPrep panel.

  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 S2_pocket_enumeration group by clicking on the group heading.
  2. Go to Tasks > Browse > Ligand Preparation and Library Design > LigPrep (3D Conversion).
    • The LigPrep panel opens.

Figure 5-7. The LigPrep panel.

  1. For Use structures from, choose Project Table (35 selected).
  2. Under Stereoisomers, for Computation, choose Determine chiralities from 3D structure.
  3. Change Job name to ligprep_enumeration.
  4. Click Run.
    • The job takes ~1 minute.
    • A banner appears and a new group ligprep_enumeration-out is added to the  Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
  5. Close the LigPrep panel.

5.2 Covalently dock the enumerated series

Figure 5-8. Opening the Covalent Docking panel.

  1. Includethe entry is represented in the Workspace, the circle in the In column is blue 5MQY – prepared 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 ligprep_enumeration-out group by clicking on the group heading.
  3. Go to Tasks > Browse > Glide > Covalent Docking.
    • The Covalent Docking panel opens.

Figure 5-9. Running the Covalent Docking job in the Virtual Screening mode.

  1. For Use ligands from, choose Project Table (37 selected entries).

 

Note: All selections in the Receptor and Reaction Type tabs will remain the same as those set in the Pose Prediction section. Confirm these settings are the same as in Section 4.1.

 

  1. In the Docking tab, for Docking Mode select Virtual Screening (Fast).
  2. Change the Job name to 5MQY_Virtual_Screening_S2_Pocket.
  3. Click Run.
    • This job takes ~1.5 hours to complete.
    • A banner appears and a new group 5MQY_Virtual_Screening_S2_Pocket-out is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

 

Note: To save time, you can use the pre-generated results. To import the pre-generated results, go to File > Import Structures and choose 5MQY_Virtual_Screening_S2_Pocket-out.maegz from the 5MQY_Virtual_Screening_S2_pocket_enumeration folder in your Working Directorythe location that files are saved.

 

  1. Close the Covalent Docking panel.

5.3 Analyze the results from virtual screening covalent docking

Figure 5-10. Setting the Workspace for analyzing the results using the Pose Viewer panel.

  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 5MQY_Virtual_Screening_S2_Pocket-out group by clicking on the group heading.
    • 38 docked poses were found, and can be viewed here.
  2. Go to Tasks > Glide > Pose Viewer.
    • The Pose Viewer panel opens.

Figure 5-11. Setting up the poses.

  1. Click Set Up Poses.
    • The first entry in the 5MQY_Virtual_Screening_S2_Pocket-out group is fixed in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
  2. Use the left and right arrow keys to step through the poses and compare them.
    • For each pose, a covalent bond successfully formed to CYS 25.
    • Notice the covalent bond attachment point for the new scaffold is slightly different from that of the crystal structure.
  3. Close the Pose Viewer panel.

Figure 5-12. Comparing the poses.

Optional: For comparison, you can fix the 5MQY – prepared entry (crystal structure) in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed when looking at the poses of this new scaffold enumeration. Choose the visualization that is most helpful to you. For example, we have colored the new scaffold enumeration poses in pink, while the 5MQY crystal structure ligand is colored in gray.

 

Note: For information about virtual screening analysis please see the Structure-Based Virtual Screening using Glide tutorial.

6. Conclusions and References

In this tutorial, you learned about covalent docking modeling preparation and analysis. You further learned how to set up and analyze a Pose Prediction covalent docking job, as well as a Virtual Screening docking job with enumerated substituents using the Covalent Docking application. You also were able to visualize and analyze the docked output of both jobs.

For further reading:
  • Covalent Docking User Manual
  • Publications and Website link
  • Virtual Screening ­Toledo Warshaviak, D.; et al. A Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands, 2014,  J. Chem. Inf. Model., 54(7):1941-50
  • Pose Prediction and Scoring­ Zhu, K.; et al. Docking Covalent Inhibitors: A Parameter Free Approach to Pose Prediction and Scoring, 2014, J. Chem. Inf. Model., 54(7):1932-40
  • Case Study Bernd Kuhn.; et al. Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors, 2017, J. Med. Chem., 60(6): 2485-2497

 

 

7. 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

incorporated - once a job is finished, output files from the Working directory are added to the project and shown in the Entries and Project Table

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

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 that files are saved

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