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.
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
How to install the DockingPie plugin on PyMOL?
DockingPie  is a plugin of PyMOL  made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
[Tutorial] Installing Pyrx on Windows.
How to install Autodock4 on Ubuntu?
What values are considered as good or bad in computational docking?
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters
Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins. Zinc atoms must be considered by a force field during the docking process. In this article, we are going to dock zinc metalloprotein with a ligand using Autodock Vina . (more…)
How to generate config file for docking using Autodock Tools?
How to install Autodock on Ubuntu (Linux) with CUDA GPU support?
Autodock  is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU  provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)
Autodock Vina: Uses & Applications
Autodock Vina  is one of the most widely used bioinformatics software for computational docking. For beginners and those who are new to the field of bioinformatics, such software may appear confusing without having an initial idea of what this software actually used for. In this article, we have discussed some of the primary uses and applications of Autodock Vina software. (more…)
How to perform virtual screening using Pyrx?
How to perform metal ion-protein docking using idock?
How to install idock on Ubuntu?
idock  is a multithreaded software based on Autodock Vina. It is a virtual screening tool for flexible ligand docking. It also supports 27 different chemical elements including zinc, magnesium, iron, calcium, etc. In this article, we are going to install idock on Ubuntu. (more…)
How to analyze HADDOCK results using Pymol script generated from PRODIGY?
Installing PatchDock on Ubuntu (Linux)
PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It performs molecular docking of any two types of molecules including proteins, DNA, drugs, and peptides. In this article, we are going to install PatchDock on Ubuntu (Linux). (more…)
Protein-protein docking using HADDOCK2.4 web server
HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/)  is used for protein-protein docking and their modeling. Not only proteins, but it can also process peptides, small molecules, and nucleic acids. In this article, we are going to perform protein-protein docking. (more…)
How to perform site-specific docking using Pyrx?
How to install sdsorter on Ubuntu (Linux)?
sdsorter is a tool that helps in the easy manipulation of SDF files. It takes a single file as input and also provides a single output file. In this article, we are going to install sdsorter on Ubuntu (Linux). (more…)