Previously, we have provided a tutorial on saving good-quality images using Pymol GUI. In this article, we are going to save high-resolution images using the Pymol...
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...
Snakemake is a workflow management system to create scalable data analyses [1]. Workflows are defined in Python-based language. In this article, we are going to install...
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...
HMMER [1] is a well-known bioinformatics tool/software. It offers a web server and a command-line tool for users. Here are some additional applications of HMMER.
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...
Modeller is a standalone tool for homology modeling or comparative modeling of proteins 3D structures [1-4]. In this article, we are discussing its different uses and...
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...
Autodock-Vina-develop [1,2] package offers some extra features in addition to Autodock Vina. It includes AutoDock 4.2 and Vina scoring functions, a batch mode for virtual screening...
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...
A new toolkit called CoolBox is developed for the visual analysis of genomic data [1]. It makes it easy to visualize patterns in a large-scale genomic...
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...
Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this article, we are going to install this software on Ubuntu.
An automated workflow for single nucleotide polymorphisms detection is developed. This is known as OVarFlow [1]. This workflow also helps in the identification of insertions and...
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...
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