Docking
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1.jpg)
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
DockingPie provides a great interface to perform docking such as Pyrx. However, the advantage of using DockingPie is that you can directly import structures from PyMOL, you can perform virtual screening including flexible docking, and easily analyze docking output data.
The installation of the DockingPie plugin is explained in this article. After the successful installation, you can select which algorithm you would like to use for docking as it offers four different algorithms for docking, namely, Vina, RxDock, SMINA, and ADFR. Here, we will use Vina.
These are the steps involved in performing docking using DockingPie.
Preparing Receptor
- Open PyMOL.
- Open the PDB structure of a receptor and a ligand that you would like to dock.
- Go to the ‘Plugin Manager’ –> ‘DockingPie1.2’.
- Go to the appropriate tab of the docking algorithm (here, Vina).
- Under the ‘Receptors’ tab, click ‘Import from PyMOL’. It will prompt you to select the receptor. Click ‘Import’ after selecting the receptor. You can open multiple receptors as well.
- Under ‘Receptor settings’, you will see the receptor. Check the receptor. It will enable some other options to select such as adding hydrogen, deleting water, and removing all NON-standard residues. Check all of them.
- Then click on ‘Generate Receptor’.
- In a small box on the right, the receptor name will appear. Select the receptor –> click ‘Set’.
Preparing ligand
- Click the ‘Ligands’ tab.
- Repeat the steps 5 to 8.
Grid settings
Here, you have three options. You can either:
- extract the binding pocket as an object in PyMOL, or
- copy a configuration file, or
- set the grid dimension by changing the coordinates values.
If you want to solely perform docking in PyMOL, then choose option 1. If you already have a config file, then go for the second option, and if you have a grid file from Autodock Tools, then you can also choose the third option.
You can save multiple cavities at this stage. After adjusting everything, click ‘Set in Docking Tab’.
Running Docking
- Click the ‘Docking’ tab. You will see your prepared receptor and ligand (see below).
- You can select the Docking type. Here, we are using ‘ALLvsALL’. You can select custom as well.
- Select the saved cavity from the dropdown.
- Select the receptor and ligand.
- Set other parameters such as the number of poses, exhaustiveness, and energy range.
- At this point, you can select flexible docking by defining the flexible residues.
- Now, click ‘Run Docking’.
It will take a few minutes to finish docking.
Analysis
- Click on the ‘Results’ tab. Here, you will see all generated poses along with their binding affinities and RMSD values (see below).
- Here, you can do several operations such as plotting the RMSD values of the docked ligand and the reference ligand (you will have to open a reference ligand in PyMOL).
- You can see all log files by clicking on ‘LOG Files’.
Besides, you can see the consensus scoring of two or more available algorithms and compare them easily under the ‘DATA ANALYSIS’ tab. You can visualize them as a matrix and export them into .csv format.
This is the basic tutorial. You can explore and perform more operations.
References
- Rosignoli, S., & Paiardini, A. (2022). DockingPie: a consensus docking plugin for PyMOL. Bioinformatics, 38(17), 4233-4234.
- The PyMOL Molecular Graphics System, Version 2.5, Schrödinger, LLC.
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn-400x240.jpg)
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn-80x80.jpg)
DockingPie [1] is a plugin of PyMOL [2] 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.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
After performing computational docking, a question that comes to mind most is “what docking score is considered good or bad”. In this article, we will discuss this in detail. (more…)
Bioinformatics Programming
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 (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?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn.jpg)
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 [1]. (more…)
A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)
Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)
Autodock Vina [1] 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…)
Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article, we are going to perform virtual screening using Pyrx. (more…)
Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article, we are going to demonstrate the docking of a metal ion (such as Zn, Mg, Fe, etc.,) with a protein using idock. (more…)
idock [1] 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…)
In one of our previously published articles, we demonstrated protein-protein docking using HADDOCK2.4 [1]. In this article, we are going to demonstrate the HADDOCK results analysis using a Pymol script generated from the PRODIGY server [2]. (more…)
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…)
HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/) [1] 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…)
Pyrx [1] is a virtual screening software that allows the docking of multiple ligands with a target protein. Previously, we provided an article on the installation of Pyrx in Ubuntu. In this article, we are going to perform protein-ligand docking using Pyrx. (more…)
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…)
Docking
Video Tutorial: How to use vs_analysis Python script for virtual screening result analysis of Autodock Vina?
This is a demonstration video of our previously mentioned Python script (vs_analysis.py) for virtual screening results analysis of Autodock Vina. (more…)
Antigen-antibody interactions play an important role in protecting our body from foreign molecules. This is applied in vaccine development against a disease. In this article, we are going to mention a simple methodology used in studying/ identifying interactions between antigen-antibody complex. (more…)
You must be logged in to post a comment Login