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How to perform blind docking using AutoDock Vina?

in Docking/Drug Discovery/Softwares/Tools by

Blind docking is done when the catalytic/binding residues are unknown in a protein, hence, the binding pocket is unknown. In a previous¬†article, we showed how to perform site-specific docking using Autodock Vina, where we bound a ligand in a catalytic pocket of a protein. Now, this article will cover the blind docking using Autodock Vina. Continue reading “How to perform blind docking using AutoDock Vina?” »

How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?

in Phylogenetics/Softwares/Tools by

If you want to get a quick idea about the non-synonymous vs synonymous (dN/dS) substitutions, you can easily use MEGA software [1]. Although HYPHY/Datamonkey provides the best results regarding selection pressure analyses. MEGA also uses HYPHY program [2] to calculate the dN/dS substitutions rate. Here is how you can do it. Continue reading “How to calculate dN, dS, and dN/dS ratio on a set of genes using MEGA?” »

Installing Roary and Prokka on Ubuntu

in Softwares/Tools by

In the last article on Bioinformatics Review, the utilization of Roary [1] and Prokka [2] was explained to create a pangenome from isolated genome sequences. This article is about installing these both packages on Ubuntu. Continue reading “Installing Roary and Prokka on Ubuntu” »

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