Receptor Settings

To configure receptor binding sites, navigate to the Receptor tab and select the binding site components.

1. Protein Chain Selection

• Select one or more chains that make up the binding site.

• While selecting all chains is possible, it is recommended that you select only the chains that make up the binding site for ease of use.

• If you have selected a ligand, you can use the left 3D viewer to select the chains adjacent to the ligand.

• This example selected chains A and D adjacent to the ligand as components.

2. Cofactor Selection

• Scroll down to find the cofactor section.

• The second part contains information about cofactors. If a cofactor is located near the binding site and may influence drug binding, select it.

• Hyper Lab automatically recognizes and selects ligands and cofactors, but there can be exceptional cases, so please ensure the settings are correct.

• In this example, the cofactors A-MG-201, A-GCP-202, D-MG-201, and D-GCP-202 are present but were not selected because they are located far from the binding site.

If you want to see the details of cofactors' binding information, click the magnifying glass icon next to each component's name.

In the case of a multichain PDB structure, cofactors may be present in each protein chain. Please ensure that the cofactors you intend to use are located at the binding site of the selected protein.

The cofactor list contains ligands as well. Selecting a ligand as a cofactor may lead to incorrect results.

Please ensure that ligands are deselected in the cofactor list.

3. Water molecule selection

• Scroll down to find the water molecule section.

• If you have loaded a protein structure using a PDB ID, it often includes water molecules. The position of these water molecules can be important, and if they significantly affect the actual ligand interactions, you can include them.

• In the example above, water molecules do not influence the target protein-ligand interactions, so they were not selected.