Researchers working in the field of bioinformatics are well-aware of the word “coordinates” in the context of docking. However, it could be a little difficult to understand the concept of coordinates in docking for beginners and experimental biologists. This is a small article to explain the meaning and role of coordinates in computational docking.
While we are performing docking whether blind or site-specific docking, we need to read the macromolecule into the software (such as autodock tools). After that, we have to specify the location for docking within the protein. If you are going for blind docking then you can select whole protein. If you are going for site-specific docking, then you need to specify a particular pocket. For this purpose, docking programs such as Autodock Vina use a special feature called grid box.
The grid box is an adjustable three-dimensional box displayed on the GUI of autodock tools. It is adjusted such that it encloses the binding pocket/selected binding residues completely. Here come the coordinates. Coordinates are the basic x, y, and z coordinates as you have read in geometry. They point to three different directions in space and define a location. You must have noticed that the coordinates change whenever you move/adjust the grid box while defining the binding pocket.
In the context of docking, location refers to the binding pocket and space is the protein surface. These coordinates do not have any unit and they are either positive or negative. In Autodock Vina, they are called “center coordinates” and are ultimately written in the configuration file. You must have seen some decimal numbers written in the file. They are coordinates for docking at a specific location. You can adjust them depending upon the binding pocket in your receptor.