Binding Site Settings

The process involves selecting the components of the target protein's binding site. You can choose various elements that might influence protein-drug binding, such as binding site residues, cofactors, and water molecules.

• When you load a protein structure, as shown in the figure below, you can see the 3D structure of the protein in the 3D viewer on the right and information for setting up the binding site in the lower section. In the Binding site tab on the right, you can set the location and size of the binding site.

• There are three methods to set up the binding site.

METHOD 1. Configuring with ligands bound to the protein structure

• Configure the binding sites by selecting ligands bound to the protein from the imported structure.

• In the Ligands section, when you select the ligand to be used as a binding site, the ligand structure and binding site box will appear automatically.

• The example below shows how we configured the binding site based on the selected ligand A-R6W-203.

METHOD 2. Configuration of the binding site based on residues

• It is the configuration of the binding site box by selecting one of the residues that make up the binding site.

• This method can be used to define the binding site using an approximated box approach.

• When we click on Select residues, we can see the residues that make up each chain.

• When we select the residues that make up the binding site, we can see the residue structure and binding site configuration box in the 3D viewer.

• However, the configured box size is too small to use.

• In this case, we could select the multiple residues to configure the binding site.

• By clicking on Select multiples, we could choose two or more residues to the configure binding site.

The binding site box configured using residue selection may not accurately represent the actual binding site. Please refer to the section on adjusting box location and size to fine-tune your binding site box as needed.

METHOD 3. Upload binding site ligand to configure binding site

• This method configures the binding site box using a file containing ligand structure information. It can be used when you have a structure file of a ligand bound to the binding site.

• By clicking on Ligand upload in the upload section, the Select a file icon is activated.

• Clicking Select a file opens a window.

• By selecting the ligand location file and clicking open, the ligand structure appears alongside the protein structure, and the binding site box is also displayed.

The supported ligand location file extensions are: PDB, SDF, MOL2

Please note that the ligand is located in the binding site before proceeding to the next step.