3D & Analyze Page

Note

The new 3D & Analyze page offers a streamlined approach to data analysis by combining the tools from the previous 3D Modeling and Analyze pages into one page. Users can now visualize and analyze data without moving between different pages. Keyboard shortcuts allow you to switch easily between preset layouts that previously were on different pages.

The 3D & Analyze page provides several ways to examine and interact with data.

The 3D Viewer allows the user to interact with and edit molecular structures, examine docking results, perceive protein-ligand interactions, and edit ligands in the context of the active site. Data trees accompanying the 3D Viewer show molecules, proteins, and related information such as constraints.

The 3D & Analyze page also includes an interactive molecular spreadsheet. It allows typical actions such as column sorting, pinning, and choice of selected rows.

Graphing capabilities offer several plot types, including scatter, boxplot, and histogram, as well as robust multi-linear regression. The 3D Viewer, spreadsheet, and plots are connected such that a molecule selected in one is also active in the other two.

Numerous cheminformatics functions are available, such as substructure search, R-group decomposition, and property calculation. Floes to calculate new properties for plotting and regression can be called directly from this page.

_images/3d-analyze_view.png — **Figure 1.** The 3D & Analyze page showing the 3D Analyze view plus the Data & Columns panel. Different views can be toggled using keyboard shortcuts or via the Layouts drop-down. In this case, the Data & Columns panel was added to the preset 3D Analyze view by clicking on “data & columns” in the Layouts drop-down.

Table 1. Important Features of the 3D & Analyze page.

Name	Description
3D Viewer	Displays 3D structures of small molecules, macromolecules, design units, and other 3D objects.
Spreadsheet	Displays imported data, molecular structures, and images. Users can include a variety of column options and calculated properties, such as PSA and XLogP.
Plot	Allows users to create plots. The plot type (scatter, boxplot, heatmap, histogram, or violin) can be selected from the Plot drop-down menu.
Data & Columns Panel	Allows users to compute molecular properties, perform R-group decomposition, and predict properties using a regression model.
Active Data Bar	Offers a variety of tools, including the rapid switching between active datasets, filtering, data handling, and managing page layouts.
Layouts Drop-Down	Allows users to customize the panels on the page, including preset views (3D Analyze, Analyze, and 3D Modeling). Other layouts or features can be added via click or drag-and-drop.
3D Viewer Toolbar	Allows users to fit objects in the Viewer, style molecules and proteins, change mouse modes, perform measurements, edit small molecules, select protein interactions, and generate and manipulate a binding site of a selected receptor.
3D Viewer Data Trees	Allow users to view and utilize molecule information in the 3D Viewer. These lists include All Data, Focused Data, Pinned Data, Large Molecules, Visible Records, and Visible Objects.

Data Panel Shortcuts

Four primary data panels are available on the 3D & Analyze page: 3D Viewer, Spreadsheet, Plot, and Data & Columns. Three preset views are offered under the Layouts drop-down: 3D Analyze, Analyze, and 3D Modeling. Clicking on the Layouts button brings up all possible panel options and selecting a panel will add it to the screen. Clicking the X in the corner of a panel removes that panel from the current page view.

Note

Keyboard shortcuts can be used to easily switch between default views.

Table 2. Keyboard shortcuts for toggling 3D Analyze views.

Mac Keyboard Shortcuts	Windows Keyboard Shortcuts	Layout View	Panels
Option + 1	Alt + 1	3D Analyze	3D Viewer, Spreadsheet, Plot
Option + 2	Alt + 2	Analyze	Spreadsheet, Plot, Data & Columns
Option + 3	Alt + 1	3D Modeling	3D Viewer

With a variety of movable panels that can be selected, hidden, or resized as needed, the 3D & Analyze page offers maximal flexibility for examining data.

_images/3d-analyze_hotkeys.png — **Figure 2.** The Layouts drop-down showing Mac keyboard shortcuts for 3D & Analyze page views. See Table 2 above for Windows shortcuts.

Active Data Bar

The Active Data Bar contains several useful drop-down menus and features. It allows the selection of active datasets, filtering of records, data handling, layout options, and more. The Data page also contains an Active Data Bar.

Active Datasets

The Active Datasets drop-down allows rapid selection of and toggling between multiple datasets. If no datasets are activated, then no data will be populated. To browse datasets, click the Active Datasets drop-down.

If a dataset is listed, click the corresponding checkmark under “Display” to display it.
If the dataset is not listed, type the name into the Quick Search bar, or click the “Browse” button to select a dataset from the Data page.
For each dataset in the Active Datasets drop-down, you can check “Display” to show all data in that dataset or uncheck to hide a dataset without deactivating it.
The “3D Only” option allows for data to be hidden from the Spreadsheet and the Plot while still appearing on the 3D Viewer and 3D Viewer data lists. This may be useful when working with docking results, in order to hide extra columns that are part of a DU but not part of each molecule in a docking hit list. A dataset that is selected as “3D Only” will appear in the Focused Data list. It also excludes that dataset from any filtering.
Individual datasets can be cleared by clicking the X, and all datasets can be cleared by selecting the “Clear All” button.

Filters

Using the Filters drop-down, two types of filters may be applied to the active and displayed datasets. The number of active filters is shown on the Active Data Bar.

Note

For all filter queries, the “Enabled” box must be checked to filter all molecules that are active and displayed. The “Invert” checkbox filters all active and displayed molecules that do not have that substructure.

Enabled filters from previous queries on any active datasets will appear in the drop-down and will be applied to all active and displayed datasets.

To apply a filter, click on the Filters drop-down, then the ‘Choose a Filter’ box. Two categories will be available, substructure and column. Any previous or current substructure filters and all column options will be visible. Enabled filters for each category can be collapsed.

The first type of filter is a substructure filter. For a new query, click on the New Query button to open the Sketcher; a query name is required to search for that substructure.

The second type of filter is based on data in the columns of the related spreadsheet. These filters (columns) vary with the dataset and may include data such as molecular weight, heavy atom count, and Tanimoto combo score. Some qualities, such as molecule or PDB, offer an option to enter a query name; a name must be provided to apply the filter. For others, such as chiral centers or Tanimoto combo score, a value or range of values must be provided. Certain column filters give the option to view the information in a list or visualize it in a histogram.

_images/3d-analyze_filters.png — **Figure 5.** The Filters drop-down. A. Drop-down with filter options collapsed. B. Available filter options, including existing substructure filters, an option for a new substructure filter query, and column filters. C. Expanded filter options showing the details and enabled status of existing filters. Along the top, the Active Data Bar shows the active versus total filters (2/3), the number of records filtered (657), and the number passing filters (19).

Categorical string fields can be filtered using a “free text” setting. This allows creation of filters that can match multiple distinct categorical values that contain a provided string.

Records

The Records drop-down includes three parts: All, Passing Filters, and Selected. The number of records that match each part is displayed at the top. The All drop-down allows for working with all of the active datasets, whether they are displayed or not; these records can be sent to a floe, saved to a new dataset, or appended to an existing dataset. The Passing Filters drop-down allows for tagging, sending to a floe, saving to a new dataset, or appending to an existing dataset only the records that pass a chosen filter. The Selected drop-down is similar to the Passing Filters drop-down, but is only for records that are highlighted and selected.

Snapshot Link

The Snapshot Link option allows you to create a link to the current state of the 3D & Analyze page, either to share that page with other project members or to return to the same state after switching to a different project or task.

Discussion Boards

You often need to share data and discuss the results with team members. Discussion boards are accessed by the “chat” icon on the Active Data Bar. This drop-down allows you to create and access your discussion boards. They are organized by project name and are also available on the Data page. Discussions are preserved so you can revisit them. The discussion board autosaves users’ edits.

You can share links and images along with text comments. A snapshot from the 3D & Analyze page can be included on a discussion board. Snapshot links can be added in two ways. First, you can select text while writing a discussion comment and click the ‘Snapshot link’ tooltip. This link style will open in the same tab as your current session. Alternatively, you can click the Snapshot icon in the Active Data Bar and paste it into the comment: that link will open in a new tab.

For more information, see the training video for using discussion boards.

Data Handling

Spreadsheet data can be manipulated using the Data Handling feature to specify various aspects of the data, such as whether certain columns are visible or not. It also enables a style to be chosen for treating imprecise data (f, ranges, inequalities, and multiple values). Records occasionally state that the dataset has hidden fields. In this case, hidden fields can be selected through the Data Handling feature. Hiding fields can make data analysis easier in some situations.

Layout

The Layouts drop-down allows users to choose the panels on the page, including both standard layouts and custom options that can be clicked or dragged onto the page. These layouts will be familiar to experienced Orion users.

As shown in Table 2, keyboard shortcuts allow you to easily toggle between the preset layouts. For Windows machines, use Alt rather than Option.

Option + 1: 3D Analyze (Default view)

Option + 2: Analyze

Option + 3: 3D Modeling

Spreadsheet

The Spreadsheet allows typical actions: column sorting, pinning, reordering or deleting, and choice of selected rows. Pop-out views of structures are also available by clicking on the magnifying glass icon.

The spreadsheet data can be manipulated by the Data Handling feature that permits a user to specify various aspects of the data, such as whether certain columns are visible or not. It also enables a style to be chosen for treating imprecise data (for example, ranges, inequalities, and multiple values). Data Handling shows data completeness for each column, as well as what type the column is (string, int, float, etc.). This feature can be accessed from either the Active Data Bar or the ‘Column Options’ drop-down in the Spreadsheet.

Hint

The Data Handling feature allows users to apply column settings to all data columns of the same name for all displayed datasets.

Spreadsheet cells can be copied to the clipboard, sent to other tasks in Orion, rated, or tagged.

_images/3d-analyze_spreadsheet_with_menu.png — **Figure 6.** Spreadsheet cells can be manipulated for further use in Orion. To access this menu, right-click in the desired cell.

JSON data fields are viewable in the spreadsheet.

Cells in the Spreadsheet are tethered to points on the plot and also to 3D representations in the 3D Viewer. The 3D molecules can be overlaid with the query molecule if desired. In addition, pinned records in the 3D Viewer also are pinned in the spreadsheet and vice versa.

This video shows some basic capabilities of the spreadsheet and the graphing feature.

Plot

The graphing feature can represent data with five different variables, some categorical and some continuous, via the choice of point shapes, size, color, and x and y values. Scatter plots, box plots, histograms, heatmaps, and violin plots are available, where appropriate, for the selected data type(s). Multiple graphs can be created. Points can be selected by lasso or by point-and-click. Depictions of structures can be accessed for any selected points. The graph can be moved, panned, or reset. Scales can be changed from linear to log forms. Regression lines (with error bars) can be added. Box plots contain quartile ranges and other annotations. A screenshot of the plot can be taken and downloaded by clicking the camera icon located above the Plot panel.

Data & Columns

This panel offers numerous cheminformatics functions, such as R-group decomposition, property calculation, and a robust multilinear regression feature. Floes that calculate new properties are also available from this panel.

3D Viewer

The 3D Viewer allows the user to interact with and edit molecular structures, examine docking results, perceive protein-ligand interactions, and edit ligands in the context of the active site. Larger panels can be moved, hidden, and resized, which is useful for closer visualization of the 3D window when needed. Also, some features of the 3D Viewer are collapsible: the data tree lists, the 2D depiction of small molecules, and the sequence viewer. Simply click the sideways caret next to the desired feature to collapse or expand it.

3D Data Tree Options

Several options are available for viewing lists of molecular and protein data. Focused Data and Visible Records are new data tree options in the 2025.2 release.

Table 3. 3D Viewer Data Tree Options.

Data Tree Option	Included Records
All Data	All records, organized by dataset
Pinned Data	All pinned records
Focused Data	Pinned Data + Visible Records + 3D ONLY datasets (selected in Active Datasets drop-down)
Large Molecules	Records that include a large molecule (>255 atoms)
Visible Records	All records that have something visible in the Viewer
Visible Objects	Visible records, but filtered to show only the visible elements

Note

The Focused Data tree manages the data lists by narrowing down the records to those that are currently being examined. This may offer a cleaner appearance than the All Data tree.

Badges

Each data tree has a list of records. Each record has at least one badge (see Table 4). Badges identify molecules, design units, proteins, grids, surfaces, and components of the DU such as receptors.

The letters come from the field names (such as bl for bound ligand or DG for Density Grid). The colors correspond to the field type. The type is labeled below it. The star on a molecule badge indicates it is a primary molecule.

In general, the badge colors are designated as:

Molecule = blue
DU = green
Surface = purple
Grid = orange
Other = white

They are faded if the field is not shown.

Table 4. Common Badges.

Badge	Field Name
d	designunit
P	protein
L	ligand
bl	bound ligand
M	molecule
OM	overlay molecule
Q	query
R	receptor
IC	receptor inner contour
OC	receptor outer contour
Cn	constraints
DG	density grid
DD	diff density grid
S	solvent
PR	packing residues
Ex	excipients

For more information on badges and lists in Orion, please see this video.

How to Manipulate Record Information in the Data Trees

Visibility of Records

Note

3D controls for visibility and pinning are linked to the spreadsheet.

The green dot controls visibility of records in the 3D Viewer. To select a record, click the dot to make it green. This can be done either in the data list or in the spreadsheet.

Expand the record using the caret next to its name.
The object may need to be fitted to the Viewer window to be seen. See the Records Menu section below.
Objects in the record that also have a green check will be shown. The green checkmarks are hierarchical, so every parent object must also be checked.
Clicking on a molecule badge in a data tree list can also enable the record in the 3D Viewer.
For small molecules, you can click the molecule badge to show the 2D depiction in the lower left corner if it is not given.
For large molecules such as proteins, you can also click the checkmark next to specific aspects of the record (density grid or receptor, for example).
Hovering over the badge will show the structure of any record with “molecule” as a field type (molecules, ligands, etc.).

_images/3d-analyze_record_visibility.png — **Figure 7.** The 3D Viewer labeled to show details of record visibility and general features.

Records can be pinned by clicking the pin next to the record name in either the spreadsheet or the data list. These records populate the Pinned Records data tree in the 3D Viewer and allow you to save them as a separate dataset.

Hovering over the record name reveals a text symbol and star. Notes about the record can be added by clicking on the text symbol. Stars can be added to rate a structure.

Certain actions, such as converting a 2D structure to 3D or editing a molecule, will prompt you to save or discard changes. These options will appear by the record name as disk or refresh icons, respectively.

Records Menu

Click the arrow to the right of the green activation circle to bring up a side menu. Records that are not expanded will have only the Center and Data Operations options visible. Records with molecule as a field type also have Style, Edit, and More as options.

Center options modify the view. Center fits the object in the center of the Viewer, and Fit enlarges the object to fill the window.
Style applies styling options to the selected record only, as opposed to all records in the Styling option on the 3D Viewer Toolbar.
Edit removes any receptor features. It offers the same editing tools as other Sketcher windows but adds options for Torsions, Apply Charges, Invert Stereo, Energy Minimize, and Explore Confs. See Figure 16 for more information.
Edit a Copy allows you to edit a copy of the molecule. This option is only available for records with a Molecule (M) badge.
Data Operations allows you to duplicate the molecule to a new record or to remove the molecule from the record.
More allows you to rename the badge or to generate 3D coordinates if the molecule is in 2D.

For a brief introduction about how to visualize small molecules, see this video about Styling Small Molecules.

Convert a 2D Molecule to a 3D Conformer

Molecules in a dataset sometimes appear in 2D rather than 3D. To engage these molecules in three dimensions, it is necessary to convert them to their 3D form. While the molecule can be sent from the spreadsheet to the OMEGA - 3D Conformer Ensemble Generation Floe, it is far easier to generate the 3D coordinates directly in the 3D Modeling layout. You can determine which molecules are depicted in 2D by expanding the molecule file on the left. Molecules in 2D have a red 2D next to the molecule badges, as shown by the yellow arrow in Figure 9. Simply expand the caret, click the three-dot menu, and select Generate Coordinates. A 3D depiction of the molecule will now be available, as shown in the inset. The 3D depiction can either be saved or reverted to the 2D form.

_images/3D_generated3D_from2D_inset_lam-2.png — **Figure 9.** Molecules that are displayed in two dimensions in the 3D Viewer can be converted into 3D structures. The inset shows the generated 3D structure.

Another option for generating 3D coordinates is to edit a structure using the pencil icon in the Toolbar.

Sequence Viewer

Specific residues of a selected protein can be located and selected from a sequence viewer at the bottom of the 3D Viewer. When a residue is clicked, it is highlighted in the 3D window. Conversely, when residues are selected from the 3D Viewer menu, the residues in the sequence viewer will also be highlighted. To collapse the sequence viewer, click the arrow on the left side of the strip. To return it to view, click the arrow on the right side of the window.

3D Viewer Menu

The Viewer menu offers numerous features for analysis of small molecules and proteins.

File Tab

The File Tab allows you to import a biomolecule with a PDB ID or to upload PDB/MTZ files. It includes several options for your biomolecule.

View Tab

The View Tab fits or centers the molecule in the Viewer.

Select Tab

The Select Tab presents options for selecting or deselecting features, residues, atoms, or other subsets of the system.

Invert inverts the selected atoms; if atoms 1 through 5 out of 20 are selected and then Invert is used, atoms 6 through 20 will be selected. This applies to other selection methods like residues, chains, and so on.
Mouse Mode allows you to select portions of the Visible Object using the mouse: either Atoms, Residues, Chains, or Molecules. Selected portions will be highlighted in orange.
Expand Selection allows the current selection to be expanded. If an atom is selected in Mouse Mode, using Expand Selection to Residues will highlight all atoms of the residue containing that atom. Expand Selection to Molecules works similarly. Expand Selection by Distance opens a dialog box that allows you to select atoms within a specified distance from the current selection; there is also an option to deselect the originally selected atom(s). Similarly, Expand Selection by Connectivity opens a dialog box that allows for the selection within a specified number of bonds.
Protein allows you to select the following feature options: Residues, Backbone, Side Chains, Water, Cα, Nucleic, Disulfide Bonds, Zero Occupancy, Partial Occupancy, and Secondary Structure. Again, these will be highlighted in orange. Expand Selection to Residues or to Secondary Structure will expand the selection as indicated. Zero and Partial Occupancy refer to the crystallographic “occupancy” property of an atom in a residue. For large molecules, Zero Occupancy sections are built out by Spruce, and Partial Occupancy are built out by Spruce or manually through the 3D Viewer (see Identify Partial Residues under the Proteins option of the Modeling Tab).
Atom Features highlights features in the Visible Object such as atom numbers, charged, heteroatoms, metals, rings, chiral, and halogens.
Visible Molecules allows you to select specific records that are currently visible in the 3D Viewer. The selected record will be highlighted. To see the selected record, you may need to choose Fit Scene under the View Tab.
Combine offers three options: Include previous, Intersect previous, and Exclude previous. To use this tool, first select features (such as atoms) based on the current Mouse Mode (hold Cmd key to select several), then click into the Viewer to deselect. Now select another set of features and leave them highlighted. Intersect previous will now highlight the first set. Exclude previous will keep the second selection. Intersect previous will highlight any features in common to the two sets. This tool could be useful if you want to find two features in common. For example, select the ‘Charged’ option under Atom Features, then click in the Viewer to deselect the highlighted areas. Next, click ‘Residues’ under Protein and select a residue, such as E for glutamic acid. Without deselecting the highlights, select ‘Intersect Previous’ under Combine. Only the components in common will now be highlighted.

Modeling Tab

The Modeling Tab is especially useful for protein modification and modeling.

Overlay Selected Atoms: Superimpose molecules based on the current selection. The first molecule selected will remain fixed. For the superposition of specific atoms, select the atoms you want to overlay (on both atoms), then click Overlay Selected Atoms.
Edit DU Receptor: This feature allows you to modify a receptor grid directly from the 3D & Analyze page. Specific details for using the Edit DU Receptor tool can be found here.
Generate Analogs: Ligand analogs can be easily generated using this tool. See below for a longer explanation.
Proteins: Because protein modeling is a large topic, a longer discussion can be found below.
Modeling Floes: When floes are enabled for the 3D & Analyze page, they will be listed under this option. Clicking on the name of the floe will take you directly to the Job Form for that floe. If no floes are activated for the 3D & Analyze page, click the option Tag Floes as 3D Analyze, and you will be taken to the Floe page where you can select a floe to enable.

Tools Tab

From this tab, a screenshot can be captured, named, and downloaded to the Downloads folder. To improve the resolution of your screenshot, change the view to full screen and increase the resolution in your computer settings. The Preferences tool offers options to change the 3D Viewer, including the strength of shadows (fog), bond style, grey ribbon sides, edge preferences, background and measurement colors, default molecule and protein styles, mouse map, and selection mode. After you have made changes, click the “Apply” button. “Close” will return all preferences to the original state. You can change the location of the Toolbar or even hide it entirely.

Help Tab

The Help option provides several mouse tools, key shortcuts, and icon definitions to improve usability of simple Viewer tasks, such as using a left click-and-hold plus the Cmd key to translate the entire molecule.

Toolbar

Definitions of these tools are included in Table 5.

Table 5. Toolbar Definitions.

Tool Symbol	Tool Name	Function
	Hide visible objects	Visible objects are hidden and must be reselected from the data trees
	Center viewport	Center the view on selected atoms or the entire scene
	Fit viewport	Fit the view to selected atoms or the entire scene
	Fit previous/next	Fit to previous or next selected residue
	Style	Style the selected atoms
	Switch mouse mode	Use mouse mode options to move molecules in the Viewer
	Measurements	Use mouse mode to create measurements
	Auto-interactions on/off	Set auto-interactions
	Edit molecule	Edit the selected molecule
	Generate binding site	Generate a binding site using the protein and ligand

Hide Visible Objects

This button removes all visible records from view. Records must be reselected from the data trees.

Center and Fit Buttons

Molecules can be fit to the Viewer in various ways. Fit or center will bring an object into view. By default, it will fit to the center of mass of a single molecule or the geometric center of a scene (multiple molecules). However, if a specific atom or object is selected, the Viewer will center on the selection.

Style

As opposed to the Style option accessed from the caret menu of a single record, the Style option in the Toolbar allows for styling the appearance of all records in the 3D Viewer. The dialog box allows you to change styles, colors, labels, and more for all visible objects.

Display style affects the appearance of the atoms, such as wireframe and ball-and-stick.
Coloring options allow you to customize structures by element, formal charge, partial charge, residue, chain, and various protein components. Colors can be chosen from a prepared list or via a color wheel, and they can be applied to carbons or to all atoms.
Labels can be applied if desired. Some labels are self-explanatory, such as element or formal charge. Others need additional information:
- Index: The index of an atom, a numerical label used to identify one atom from another.
- BFactor: The estimated (isotropic) MSD in the atomic position.
- Occupancy: The estimated (fractional) population of a particular conformer.
- Alt Location: The alternate location of the residue associated with an atom.
- Map Idx: The map index of an atom, used to track equivalent atom positions.
- Implicit HCount: The number of implicit hydrogens; that is, hydrogen atoms that are not explicitly drawn out but are associated with the parent atom.
- Custom: A text box allows you to input a custom label.
Hydrogens can be turned off, or turned on for either polar or all hydrogens.
Proteins can be viewed in ribbon, Cα, or backbone style. Color options are available as above, with similar customizations as above. You can choose to either show or hide waters.
Surface Type can be turned off or set to molecular or solvent accessible views.
Surface Color can be set to curvature, electrostatic, or atom color.
Surface Opacity can also be adjusted.
Style (of the surface) can be set to solid, mesh, or points.

Switch Mouse Mode

This option includes seven different modes to manipulate the 3D Viewer.

_images/3d-analyze_mouse_mode.png — **Figure 13.** The Mouse Mode options.

Select allows you to click on atoms or bonds in the structure to highlight them.
Z rotate allows you to rotate the molecule in the Z-plane only. Cmd+Shift provides a shortcut for this menu option.
Translate allows you to click-and-hold so you can move the entire molecule without rotation. Left click-and-hold plus the Cmd button provides a shortcut.
Zoom allows you to zoom in and out on the structure. The scroll wheel also performs this task.
Z translate moves the scene forwards and backwards, which affects the view relative to the fog and the clipping panes.
Clipping pane mode controls the view. It allows you to change how much of the molecule you can see. Ctrl+hold is a shortcut. If you find that part of your molecule “disappears” into the plane when it is rotated, the clipping pane can be moved farther away.
Lasso Selection highlights a lassoed selection.

Measurements

The mouse can make specific measurements for distance, angle, and torsion. To make these measurements, select the quantity you want to measure. Click on the first atom. Then for distance, click the second atom and the distance (in Å) will appear. For an angle, click three atoms to see the angle. Similarly, for the torsion angle, click four atoms in the molecule.

Viewing Interactions

Interactions between a protein and small molecule can be viewed and selected by using the Viewing Interactions tool. Click on the icon to turn this feature on or off. To select the types of interactions you want to visualize, click the caret. At the top of the pop-up window, the protein name is listed. If more than one large molecule is active in the 3D Viewer, an arrow will appear to the right of the molecule name and a different protein can be selected. Figure 14 shows the interactions options that are available for a given protein and ligand.

_images/3d-analyze_interactions_options.png — **Figure 14.** Interactions options for a protein. The features can be selected using the checkboxes. The symbols to the right show how the interaction will appear on the protein.

_images/3d-analyze_interaction_visualization.png — **Figure 15.** A visualization of the interactions between a ligand and the binding site.

Edit Molecule

Note

Molecules can be edited directly in the 3D Viewer using the pencil icon from the Toolbar.

A structure can be edited using the pencil icon in the Toolbar, and from the side menu for a particular record. Clicking the icon brings up a “Click a molecule to begin editing” prompt. For structures with conformers, a dialog box will ask whether to discard conformers. They must be discarded in order to edit the molecule. After selecting the molecule, an additional toolbar appears to the left, as shown in Figure 16.

_images/3d-analyze_edit_molecule_toolbar.png — **Figure 16.** The Edit Molecule toolbar.

Several options are the same as those seen in other UI Sketchers. Others are described below:

Torsions: The torsion angle can be measured by clicking on a rotatable bond. The torsion angle will appear. It can be adjusted using the mouse scroll wheel. Shift+hold gives fine control over the torsion angle, and Cmd+hold changes the part of the molecule that is rotated. If the bond is not rotatable, it will not be highlighted in light green and will not show a torsion angle.
Formal charge: The formal charge can be increased or decreased by 1. Clicking +/- should automatically assign N +1 and C -1.
Invert Stereo switches the stereochemistry around a chiral atom from one enantiomer to another. If a chiral atom is shown on the 2D depiction with a wedge or a dash to represent an atom coming out of or going into the plane, the 2D depiction will reflect changes to the 3D depiction.
Energy Minimize adjusts the structure to the lowest energy configuration.
Explore Confs examines different conformers of the structure. To use this feature, be sure both that the Mouse Mode option under the Select tab is set to atoms and that the ‘Edit Molecule’ toolbar is not on the build or delete buttons. On the Viewer toolbar, choose the lasso option under change mouse mode. Lasso the portion of the molecule you want to explore. For the entire molecule, lasso the entire molecule. Next, click on the box below the “Explore Confs” box and use the up and down arrows to toggle between conformers. The number of conformers (up to 20 conformers) will be listed under the record in the data list to the left. To remove that list of conformers and explore another part of the molecule, click the back arrows at the bottom of the toolbar until the conformer list in the data list goes away.

_images/3d-analyze_explore_confs.png — **Figure 17.** An example of the Explore Confs tool. In this example, a copy of the molecule is being edited. The part of the molecule used to explore conformers is circled in yellow. Compare that part of the molecule to the same area in Figure 16 to see the difference between these two conformers (of six total).

Edit the molecule as desired. When you are finished, click “Stop” above the molecule. The edited structure can be saved or discarded using the icons next to the structure record. Saving the edited molecule reveals a text box with options to overwrite the existing record or save it to an existing or a new dataset.

For a brief demonstration, see this video about Editing Small Molecules.

Binding Site Options

Styling and visualization tools specific to the binding site of a protein and ligand can be accessed with this tool. A binding site is generated by clicking the Binding Site tool. An icon will appear in the records list next to the checkmark for the protein badge; this icon can be used to toggle the binding surface on and off. If more than one ligand or small molecule or more than one large molecule are in the Viewer, a drop-down in the pop-up window allows you to choose which ligand or protein to use. Select how to visualize the binding site by clicking the caret under the Binding Site button.

Figure 18 shows the available options for the binding site. The active site is defined by the distance from the ligand (in Å). Checkboxes allow selections to fit the view to the ligand, create a binding site surface, style the protein, show the ribbon, and show labels. Specific changes can be made with the Style tool. If Style Protein is checked, the active site residue and distant residue styles can again be selected. If it is not, these options are not available, and it is not possible to deselect the Show Ribbon checkbox. After changes are made to the binding site options, a Regenerate button will appear in the pop-up window. Clicking this button will regenerate the binding site with the new parameters.

_images/3d-analyze_binding_site_options.png — **Figure 18.** Binding site options from the Toolbar.

Binding site coloration is determined by the electrostatic potential of the protein. Potentials are calculated with OECalculateSurfacePotentials from Spicoli TK. That potential is then used to do a linear gradient such that all values less than -10 are red, blending from red to white between -10 to 0, then blending up to blue at 10.

_images/3d-analyze_binding_site_view.png — **Figure 19.** The binding site of CDK2 (5K4J) with a ligand (6QB) after being prepared through Spruce.

Views can be altered using the styling tools (both on the Toolbar and for the individual records), binding site options, interactions options, and clipping pane. The binding site can be viewed with or without the protein or interactions, with receptor inner and outer contours (see Figure 21 for an example), and with different coloration.

Modeling Features

Edit DU Receptor

The Edit DU Receptor feature allows you to modify your receptor grid directly from the 3D Modeling layout. Choose a design unit (DU), then select Edit DU Receptor on the Modeling drop-down menu.

Once you open the Receptor Editor, you can adjust the size and position of an autogenerated box that defines the confines of the receptor grid. Simply make adjustments with the controls in the Setup Box. Click the “Setup Grid” button for additional options, then click “Build Grid” to build your receptor grid and see details about the contours and constraints. See the 2023.2 highlights video for a demonstration.

The goal of Edit Receptor is to define a box enclosing the active site. The box should enclose the entire region of the active site where heavy atoms of the docking ligand can be placed. Any docked pose with any heavy atom that lies outside the outer contour of the receptor will be rejected.

If a bound ligand has been specified, a default box will automatically surround the bound ligand.

The setup box can be adjusted using the Adjust Sides and Grow/Shrink controls. Clicking on a protein residue will also automatically extend the box to enclose the clicked reside.

The Shape Site Potential is an important factor in the interaction of molecules with proteins. This option defines the inner and outer contours of the receptor. Both contours are always enclosed by the box setup. “Extends toward Protein” means that the contours will extend closer to the protein before extending out into solvent, while “Extends toward Solvent” will cause the reverse to happen. The default, Balanced, is reasonable in most cases.

From the list of molecules and design units, you can fine-tune constraints and inner and outer contours as shown in the figure below. These options are enabled by using the corresponding checkboxes. Contours can be adjusted with a slide bar.

Constraints define key interactions ligands are required to make when docking into the active site. Constraints can ensure that receptor-ligand interactions known to be associated with activity are present in a docked pose.

When adding a new constraint, you can adjust the interaction options using the toolbar on the right-hand side of the 3D Viewer. Click the plus sign to bring up the “Add a Constraint” box. As you hover over the binding site, circles will appear that correspond to atoms in your protein. To add a new constraint, either select one of these atoms or choose the “Custom” option to add a SMARTS pattern. Click the disk icon to save the DU.

When adding a custom constraint, the default sphere size is 3 Å.

_images/edit_receptor_add_constraint3.png — **Figure 21.** Adding a new constraint.

You can also add a new receptor to a DU if the DU does not have a receptor. The option to add a receptor will only appear if there is no receptor present. Most of the time, this step is not necessary.

Features for enabling and modifying constraints are covered in the 2023.1 video.

Generate Analogs

This tool provides a way to quickly generate possible 3D conformers of small molecules. It takes a molecular core and adds R groups to produce analogs.

Note

This tool is meant to find quick ideas to test. It is not all-encompassing. For a full investigation using generative chemistry, we suggest using the Generative Structure Floe Site Selection Floe. For more questions or assistance, please email OpenEye Customer Support at support@eyesopen.com.

Four methods are used to generate analogs. For more details regarding how analogs are generated, please see the Generative Design Floes.

The Near Fragments method follows the parameters and methodology of the “Graft” method; new analogs are 60–80% identical to the original molecule.
The Matched Molecule Pairs method follows the parameters and methodology of the “MMP” method.
The Sidechain Exploration method follows the parameters and methodology for the “Sprout” method, but it explores new chemical matter without any notion of reagent selection or synthetic accessibility.
The Reagents method is a non-exhaustive, quick method using four small libraries of reagents—Primary Amines, Carboxylic Acids, Aryl Halides, and Suzuki Boron—to be reacted against a user-defined portion of the original molecule. Please note that this method does not require specific chemistry to be present but instead relies on the user to determine appropriate connections for their application.

To use this tool, activate a structure for which to generate analogs. Choose a method and the structure will be displayed in a pop-up window. You must lasso a selected fragment. Click the “Use selected fragment as input” button. A set of analogs will be displayed in a separate window and can be selected as desired.

_images/3d-analyze_generate_analogs.png — **Figure 22.** Using the Near Fragments option of the Generate Analogs tool. The top image shows the selected fragment for analog generation. The lower image shows the results. They can be sorted by data fields (columns), such as acceptors or molecular weight, and viewed in 2D or 3D.

Protein Modeling

The Proteins option under the Modeling tab includes several methods for editing large molecules. From the Proteins option, rotamer and histidine states can be changed, residues can be mutated, partial residues can be identified, terminal residues can be capped and converted, and protonation states can be changed. Note that making any changes will remove receptor features.

Change Rotamer States: To change a rotamer state for a residue, select a residue, then select the Change Rotamer States tool. Changing the rotamer state will remove receptor features. To modify the rotamer state for the selected residue, use the arrows in the upper right side of the Viewer window. Once the preferred orientation is found, click the checkmark, or click the red X to cancel the change and return to the original orientation. The original state can also be reached by clicking the refresh button by the record name, or the new state can be saved by selecting the disk icon.
Change Histidine States: This procedure is like that of changing rotamer states. A histidine residue must be selected. This feature can be especially helpful to change protonation in the binding site.
Mutate Residue: To mutate a residue, select a single residue and click the Mutate Residue option. A pop-up window will appear with a table of residue options, or a residue’s code or abbreviated letter can be entered.
- One action would be to mutate the residue, then rotate it to optimize fit and interactions in the binding site.
- Because mutations can change the binding affinity, this tool can be used to test the effects of different residues in the binding site.
- Another use is if you want to use the wild (nonmutated or canonical) form of the protein that matches the crystal data.
- Generally, the mutated version is what will be used in analysis. Posit can be used with mutated versions of proteins to give possible poses of ligands. This is useful in testing against known mutations.
Identify Partial Residues: This tool corrects residues when they are missing from the protein sequence. This is important because some downstream floes, such as Molecular Dynamics floes, will fail with partial residues.
- Sometimes partial residues are outputted from the SPRUCE - Protein Preparation Floe. The Floe Report will state that the design unit contains “partial side chains.” This typically indicates that manual manipulation is required because the input file may not have enough data to give an optimal residue orientation. Select Identify Partial Residues, and if the record contains partial residues, the first residue will be highlighted, and manipulation options will appear in the top right-hand corner of the 3D Viewer. The arrows toggle between different partial residues in the structure. The Fix button will grow and build the missing side chain atoms. Click the checkmark when the partial residues are fixed or click the red X to cancel and return to the original state.
- Example: The structure 1BRS was used in the Spruce - Protein Preparation Floe. The Floe Report includes the following information:

_images/3d-analyze_floe_report.png — **Figure 23.** The Floe Report from the **Spruce - Protein Preparation** Floe.

These partial residues in the structure must be fixed in order to run successful floes downstream. Choose Identify Partial Residues to manually build these missing side chains. Figure 24 shows the window that appears with the selection of this tool.

_images/3d-analyze_partial_residue.png — **Figure 24.** Valine 45 partial residue to be fixed. You can toggle through options with the arrows at the top left. To fix the residue, click “Fix” and either accept the change by clicking the checkmark or revert it by clicking the X. Note that the residue is also highlighted in the Sequence Viewer below.

When you select the residue to be fixed with the checkmark, an information box will ask whether you want to remove receptor features. Choose Continue to build the side chain. The fixed residue will now be highlighted, as seen in Figure 25.

_images/3d-analyze_fixed_residue.png — **Figure 25.** Residue with newly built side chain.

Accept or reject the change in the box at the upper right, then revert or save it using the revert or save buttons in the record list on the left.

Cap and Convert Terminal Residues: This option identifies terminal residues that are not capped. It is described in the Spruce TK OECapTermini function documentation. The arrows toggle between different terminal residues. Clicking the Cap Term button adds an acetyl or N-methyl group, depending on whether the cap is an N- or C- terminal, respectively. The Conv Term button converts the selected residue into a terminal residue capping group. Once the preferred capping is found, click the checkmark, or click the red X to cancel the change and return to the original state.
Protonation: Most biomolecular structures have been generated with either no explicit hydrogens or only polar hydrogens. However, it may be necessary to explicitly represent and position all atoms to make appropriate hydrogen bonds. This tool allows the optimization of hydrogen bonds. As part of this tool, frozen heavy atoms can be selected and selected hydrogens for heavy atoms can be frozen or unfrozen. Frozen atoms are fixed so they do not move during the optimization process. More information on these parameters can be found in the SZYBKI application or the Spruce TK Protein Placement and Optimization section.

Sample Uses of the 3D & Analyze Page

The 3D & Analyze page can be used throughout all stages of data analysis. Here are some examples.

Use the Import Biomolecule tool under the File tab in the 3D Viewer to load a PDB structure. A good example would be 1BRS, as it contains partial residues but does not have a ligand. Fix the partial residues to make the protein suitable for modeling. If desired, you can change the rotamer states or mutate residues as well.
Run the SPRUCE - Protein Preparation Floe. Check the Floe Report and use the 3D Viewer to fix any errors to generate prepared proteins that are ready for a viable MD floe run or other downstream purposes.
Use Edit DU Receptor to move or change a binding site. This could be useful when you have turned on the Enumerate Pockets parameter in the SPRUCE - Protein Preparation Floe. This parameter enables the floe to enumerate multiple binding sites on the protein. The floe can use the Site Residue Entry parameter to do this automatically, but Edit DU Receptor allows you to control this process.
Visualize the results from the OEDocking - Dock into an Active Site for Virtual Screening Floe: a dataset of ligands that are prepared for docking.
Evaluate the output from the Protein Sequence to AI Folded Structure Prediction Floe.
Evaluate the output from a SiteHopper floe.
Evaluate the output from a Cryptic Pocket Detection floe.
The Spruce tutorial gives an excellent example of using the capabilities of the 3D Analyze page to examine and manipulate data.