Use Binding Site Ligand

Binding Site Ligand Information and On/Off Function on the Bench

You can perform Hyper Binding calculations and Hyper Design using the 3D structure of the binding site ligand activated on the Bench.

1. Displaying the Binding Site Ligand in Bench

After activating a protein in the Bench, click the View Binding site ligand button at the top of the Bench.

The binding site ligand information of the currently activated protein will then be pinned and displayed at the top of the Bench.

1.1. How to Display the Binding Site Ligand

[Note] Only proteins that meet all of the following conditions can utilize the Binding Site Ligand:

1. Proteins added after the June 19, 2025 update

2. Proteins added as a 3D structure type

3. Proteins for which only one ligand was selected in the Binding site tab during addition, or a ligand file containing only one molecule was uploaded manually

Here’s how to display the binding site ligand in Bench:

1

Add a new protein after the update on June 19, 2025.

2

When adding the protein, select the 3D structure type.

The Sequence type does not support displaying binding site ligand information.

3

In the Binding Site tab of the protein addition page, select only one ligand or upload a ligand file that contains only a single molecule.

4

Once the protein is added, activate it in the Bench.

1.2. Utilizing the Binding Site Ligand Displayed in Bench

The information of the Binding site ligand displayed in the Bench can be utilized as follows.

1. The Binding site ligand displayed in Bench is updated based on the currently activated protein. If no protein is activated in the Bench, the Binding site ligand information will not be shown.

2. The Binding site ligand data can be edited just like regular molecules, but it cannot be deleted manually.

3. The Binding site ligand information will be automatically deleted when the associated protein is removed.

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2. Hyper Binding of the Binding Site Ligand

Unlike standard Hyper Binding, the result for a binding site ligand is locally optimized based on the 3D structure input by the user.

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3. Hyper Design of the Binding Site Ligand

Hyper Design for the binding site ligand is executed based on the 3D structure of the ligand entered by the user during protein registration, allowing users to perform Hyper Design using the original X-ray structure as is.