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...
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on...
![[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)
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...
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 [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...
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...
In our previous article, we generated multiple conformers using OpenBabel. In this article, we are going to generate multiple low-energy conformers of a ligand using Avogadro...
OpenBabel [1] offers several functions including file format conversion, generation of 3D structures from smiles, and so on. In this article, we are going to generate...
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...
We have previously provided an article on the installation of the Raccoon2 plugin on Ubuntu. In this article, we are going to install Raccoon2 [1] on...
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...
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,...
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...
Docking and simulation are two of the methods that are most widely used in bioinformatics. In this article, we provide all important links to the software...
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...
Pyrx is a bioinformatics software that is used for virtual screening of a large number of compounds against targets [1]. In this article, we will install...
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 out 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...
