Docking
Most widely used software for docking results image generation
Computational docking is an important technique in bioinformatics. The docking result interpretation and representation are important as well. There are various software available for docking result analysis and offer to generate high-quality images for publications. In this article, we will mention such a few software for the same purpose.
1. Pymol
Pymol [1] is a user-friendly bioinformatics tool for macromolecules visualization. It can easily generate high-quality images at different resolutions (90, 150, and 300 dpi). The higher the dpi value, the better the image. Additionally, users can set the height and width of the image keeping the background transparent or non-transparent. You can set the background as white, black, grey, and light grey according to your display needs. You can even set the display to the publication type. Also, you can save the whole session to resume later.
2. Discovery Studio (DS) Visualizer
DS Visualizer [2] is another good software for docking analysis as well as image generation for publications. Users can easily visualize interactions between the receptor and the ligand. Additionally, label color and font can be easily set along with background color and receptor color. You can set to visualize the receptor surface including aromatic, H-bond, charge, ionizability, or solvent accessible surface (SAS). You can easily generate a 2D diagram of interactions and save it in PNG format. Further, you can save the whole session to resume later.
3. Autodock Tools
Besides docking file preparation and docking, you can use autodock tools [3] for macromolecular visualization and image generation. It can also open the Vina docking output file and you can easily analyze it. Similar to other tools, the background color can be easily set. You can represent the receptor and ligand as lines, sticks, spheres, or surface. Additionally, it supports rendering large images in TIFF format. You can also save the session for later use.
4. VMD
VMD [4] is another useful bioinformatics tool for macromolecular visualization. You can set different display styles of receptors using VMD. Also, you can set the background color as solid or gradient which gives it a nice look. Additionally, you can render the receptor in different formats such as postscript, snapshot, NVIDIA Gelato, and so on.
Further Reading
- Tutorial: Vina Output Analysis Using PyMol
- Video Tutorial: Autodock Vina Result Analysis with PyMol
- Vina output analysis using Discovery Studio visualizer
References
- DeLano, W. L. (2002). PyMOL.
- Visualizer, D. S. (2005). Accelrys software inc. Discovery Studio Visualizer, 2.
- Morris, G. M., Huey, R., & Olson, A. J. (2008). Using autodock for ligand‐receptor docking. Current protocols in bioinformatics, 24(1), 8-14.
- Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: visual molecular dynamics. Journal of molecular graphics, 14(1), 33-38.
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1-400x240.jpg)
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1-80x80.jpg)
Bioinformatics Programming
DockingAnalyzer.py: A New Python script to Identify Ligand Binding in Protein Pockets.
High-throughput virtual screening (HTVS) is a pivotal technique in drug discovery that screens extensive libraries of compounds to find potential drug candidates. One of the essential tasks in HTVS is to ensure that ligands are binding within the protein’s binding pocket. This task can be particularly challenging when dealing with thousands of docking results. To address this challenge, we present a Python script that automates the analysis of molecular docking results generated by AutoDock Vina [1] using PyMOL [2]. This script calculates the center of mass (COM) for each docked pose, compares it with a reference ligand’s COM, and identifies poses that bind within a specified threshold distance. This process is crucial in mass docking scenarios where confirming ligand binding within the pocket is necessary. (more…)
Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.
Bioinformatics Programming
vs_interaction_analysis.py: Python script to perform post-virtual screening analysis
Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py [2,3] and vs_analysis_compounds.py [4]. This time, we have developed a new Python script to simplify the analysis of VS results.
![[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 [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…)
You must be logged in to post a comment Login