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...
This is a demonstration video of our previously mentioned Python script (vs_analysis.py) for virtual screening results analysis of Autodock Vina.
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...
If you are a beginner in the field of bioinformatics, you must have heard of the term “virtual screening” (VS). In this article, we will discuss...
We have provided several tutorials on docking including both types: blind docking & site-specific docking using Autodock Vina. In this article, we are going to compare...
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...
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...
Docking is performed in different ways depending upon the requirements. In some cases, it is required to dock a covalent ligand with the receptor. In this...
Pyrx is a bioinformatics software that is used for the virtual screening of a large number of compounds against targets [1]. In this article, we will...
MGLTools2 package comes with three different tools for docking: ADFR, AGFR, and AutoSite [1-3]. In this article, we will install this package on Ubuntu.
AutoSite is a computational method and tool that is used for the identification of binding sites of small molecules in target proteins [1]. It comes with...
Flexible docking is when some residues in the interacting bodies (receptor and ligand) are kept flexible leaving the rest of the part rigid. In this article,...
Finding binding sites/pockets in a target protein is one of the important steps in docking studies. It is relatively easier to find a binding pocket in...
GalaxyPepDock is a software used for protein-peptide docking based on interaction similarity. In this article, we will install GalaxyPepDock on Ubuntu.
Virtual screening can be difficult for beginners. Here are some FAQs for starters that can help you overcome small issues.
EasyVS is a web-based bioinformatics tool that simplifies the selection of the molecular library and its virtual screening [1]. Users can easily perform virtual screening of...
We have provided several tutorials on Autodock Vina software [1] including its installation on Ubuntu. This article is a guide to installing Autodock Vina on Windows...
Several errors occur while installing MGLTools and Autodock Vina on Ubuntu. We have explained the complete process of Autodock Vina installation and docking in previous articles....
It is computationally costly to predict target proteins for query compounds or a chemical library to be run on a local computer. A new tool called...
Openbabel is used to inter-convert many file formats [1]. It is available for Linux, Windows, and MAC operating systems. In this article, we will learn how...
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