CRISPR/Cas9 is a genome editing technology trending fastly. It is used to identify CRISPR associated genes within the genomes of prokaryotic bacterias. Several tools are available...
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...
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...
Gene expression in single cells is measured using single-cell RNA sequencing technology. It helps in finding new and available cell types of different tissues and organs....
CASTp (Computed Atlas of Surface Topography of proteins) server is used to predict binding pockets and cavities in proteins [1]. It displays binding pockets precisely and...
Docking software such as Autodock4 [1] and Autodock Vina [2] require input receptor and ligand files in a specific format called pdbqt. Sometimes, preparing files using Autodock...
Variant Call Format (VCF) is a text file format used to store thousands of genomic datasets. Since these files consist of a large number of gene...
CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems [1]. In this...
SALI MODELLER [1] is one of the most widely used command-line bioinformatics software for protein structure prediction based on homology modeling. The installation of MODELLER on...
PyMol is a molecular visualization software that is freely available for education-use-only [1]. PyMol provides an interface for the visualization of small and macromolecules. Besides, it...
NCBI-BLAST+ [1] command-line tool offers multiple functions to be performed on a large dataset of sequences. Previously, we have shown how to blast against a local...
Clustal Omega [1,2] and MUSCLE are bioinformatics tools that are used for multiple sequence alignment (MSA). In one of our previous articles, we explained the usage...
Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks [1]. One of its applications is in clustering protein or peptide sequences. This is a...
Molecular dynamics (MD) simulation has become an important methodology in research covering systems consisting of millions of atoms. We have provided several articles on MD simulation...
Molecular dynamics (MD) simulation is an important step in studying the dynamics of macromolecules. In one of the previous articles, MD simulation of chain A of...
This is a video tutorial of our existing article on GROMACS (Abraham, et al. (2015)) installation.
We have compiled all articles on docking into a Special Issue. This is a complete guide on molecular docking using Autodock Vina for beginners. It includes...
Virtual screening is used to identify small molecules that are most likely to bind to a target protein. There is various software available for virtual screening...
In our last article, we explained the installation of LigPlot+ [1] on Ubuntu. In this article, we will perform protein complex analysis using LigPlot+.
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