PyMol is one of the most widely used bioinformatics software. Generally, it is used as a molecular viewer to visualize macromolecules and small molecules. In this...
We have provided several articles on Vina [1] installation on Ubuntu including video tutorials. In this article, we are going to install Autodock Vina on Mac...
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...
SWISS-MODEL [1] is a bioinformatics tool that is widely used for protein structure prediction. In this article, we are going to discuss its uses and applications.
Previously, we have provided an installation tutorial for IQ-TREE on Ubuntu. In this article, we are going to perform model selection for a dataset using the...
Pymol [1] is a Python-based molecular viewer that is used for multiple purposes. We have provided several tutorials on Pymol. In this article, we are going...
IQ-TREE [1] is a bioinformatics software for phylogenetic/phylogenomic inference. It is available as a webserver and a standalone tool. In this article, we are going to...
Pymol [1] is a molecular viewer that is mostly used for visualization purposes. Besides that, it can perform several other tasks such as mutagenesis. In this...
Conda (Anaconda, Inc.) is an open-source dependency, package, and environment management system for any language such as Python, R, Javascript, C/C++, and so on. In this...
Modeller-10.1 [1, 2] is the latest version of the software. We can perform multiple tasks using this software including homology modeling, comparison of alignments and structures,...
MODELLER is a software package that is generally used to predict protein three-dimensional structures [1,2]. It can be used for some other tasks such as comparative...
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...
I-TASSER [1] is another most widely used bioinformatics software. It is used for protein three-dimensional structure modeling. In this article, we are going to discuss its...
Trimmomatic is a read trimming tool for Illumina NGS data [1]. It is a flexible tool providing several functions to be operated on reads. These functions...
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...
GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is...
Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this article, we are going to install this software on Ubuntu.
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...
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