2024-03-08 Release Note

The update for Hyper Lab on March 8, 2024, has been completed.

Hyper Lab Version : 2024.03.08

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Changelogs

1. User Fields newly added

In the Molecule list of My bench, a new type of 'User fields' has been added, allowing users to create their fields to edit and manage data.

User fields, like the existing fields provided, can be sorted, filtered, and viewed in the same manner.

(1) Creating a New Field

'Create a new field' button

User fields can be managed from the right-side screen that opens when you click the 'Field' button at the top of the Molecule list.

At the bottom of the right-side screen, you can create a new user field by clicking the 'Create a new field' button.

Create a new field

• Enter the name for the new field and select the type of field to add it to the Molecule list.

• Each field name must be unique and cannot be duplicated.

• The field type can be selected from text, number, or tag only. (Expansion of types to be provided later is planned.)

(2) User Field Editing

Users can edit and manage the fields they have created.

The methods to enter the field editing screen are as follows:

• Method 1) Clicking the [More (…)] button on the user field added to the Molecule list and then clicking [Edit field] will open the field editing screen on the right.

Field Editing Side Modal - Method 1

• Method 2) Clicking on a user field in the right screen that opens after clicking the [Fields] button at the top of the Molecule list will switch to the field editing screen.

Field Editing Side Modal - Method 2-1

Field Editing Side Modal - Method 2-2 (switch to the field editing screen)

In field editing, you can change the field's name, change the type of the field, and delete the field.

[Changing Field Type]

The type of the field can only be changed to a type that is possible to switch from the existing type.

• Text type field → Can only be changed to numeric type

  • If the original field contains a mix of numeric data and text data, conversion is not possible.

• Number type field → Can only be changed to text type

• Tag type field → Can only be changed to text type

[Deleting Field]

[Deleting Field] button

Fields can be deleted using the [Delete Field] button located at the bottom of the field editing screen.

If a field is deleted, all data stored in that field will also be deleted.

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2. 3D Viewer Improvements

The 3D Viewer has been enhanced to allow for the use of a wider range of features.

(1) Addition of 2D Diagram

Light mode

Dark mode

In the 3D Viewer, the 2D Diagram has been improved to allow viewing of interactions in a 2D structure as well.

• Each interaction is displayed differently based on the settings in the existing control panels on the left and right.

• By clicking the Pin icon at the top right of the 2D Diagram, you can control the display of indexes for each type of interaction.

(2) Viewer Setting Enhancement

The settings of the 3D Viewer have been refined to enable more detailed analysis.

[Binding Pocket Display]

Categories	Description
Sidechains	You can view the sidechains.
Surface near Clipping	It hides atoms starting from the closest to the viewer in the structure.
Surface radius Clipping	In the 3D viewer, it hides atoms starting from the farthest from the center of the molecular structure.
Surface Opacity	It adjusts the opacity of the protein surface.
Pocket radius	It adjusts the display radius of the protein residues.
Residues with ligand interactions	You can only see residues interacting with the molecule.

[Interaction Entities]

In the 3D View and 2D Diagram, you can set the following major interaction categories.

• Receptor-Ligand

• Ligand-Ligand

• Receptor-Receptor

• Ligand-Water

• Receptor-Water

[Interaction Types]

The types of interactions that can be observed in the 3D View and 2D Diagram are as follows.

Categories	Description
Covalent	Covalent bond between receptor and ligand.
Clash	When the distance between two atoms is less than the sum of their covalent radii.
Vdw	When the distance between two atoms is less than the sum of their van der Waals radii plus 0.1Å.
Hydrogen bond (hbond)	When the distance between the hydrogen (H) attached to the Hbond donor (D) and the acceptor (A) is less than the van der Waals radius of A plus 1.3Å, and the angle of D-H-A is greater than 90 degrees.
Weak hydrogen bond	When the distance between hydrogen (H) attached to a weak Hbond donor (wD) and the Hbond acceptor (A) is less than the van der Waals radius of A + 1.3Å, and the angle of wD-H-A is greater than 130 degrees.
Ionic	When the distance between the pairs of positive and negative-ly ionisable atoms is less than 4.0Å.
Metal	When the distance between the Hbond acceptor and the metal atom is less than 2.8Å.
Hydrophobic	When the distance between two hydrophobic atoms is less than 4.5Å.
Cation-Pi	When the distance between the center of the positively ionisable atom (A) and the aromatic ring (AR) is less than 4.5Å, and the angle between the straight line connecting the A and center of AR and the perpendicular of AR is less than 30 degrees.
Pi-Pi	When the distance between the centers of two aromatic rings (AR) is less than 6.0Å. Also, when dihedral angles of them, and the angle between the straight line connecting the centers and the perpendicular line of one AR are each less than 90 degrees.

[Binding Pocket Residues]

Categories	Options	Description
Structure	Type	You can view in Stick and Ball and Stick forms.
Stick radius	The radius of the Stick can be adjusted.
Color Type	You can select the color for the Binding Pocket Residue. The protein's color can either follow the dependent color scheme or be custom specified.
Label	Type	The display style of the Label can be viewed in both 1 letter and 3 letter formats.
Size	The size of the Label can be adjusted.
Color	You can choose the color of the text displayed on the Label.
Background	You can select whether to display the Label's background.
Background color	When selecting the Label's background, you can choose the background color to be displayed.

[Protein]

Options	Description
Type	You can select the viewing type for the protein. If you select Surface, you can set the Type and Color type of the protein surface, as well as its opacity.
Color by	You can specify the criteria for assigning colors to the protein. If you select Custom, you can assign colors directly.
Hydrogens	Hydrogens are displayed in the Viewer.
Water	Water is displayed in the Viewer.

[Ligand]

Categories	Options	Description
Structure	Type	You can select the viewing type for the ligand.
Stick radius	You can adjust the radius of the stick.
Surface	Type	You can select the viewing type for the ligand surface.
Color by	You can specify the criteria for assigning colors to the ligand.
Opacity	You can adjust the opacity of the ligand surface.

(3) Ligand Display Function Added

A function has been added to the Ligand Display panel, located on the right side of the Viewer, allowing you to set colors for each of the conformers.

(4) Viewer Screenshot Function Added

By clicking the [Screenshot] button on the top left of the Viewer, you can obtain the current view of the Viewer as a PNG file.

The files are provided separately for the 3D Viewer and the 2D Diagram.

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Bug fix

Bug fixes and stability improvements have been made.