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...
Circular RNAs serve as markers for diagnosis and therapeutic targets of several diseases such as cardiovascular diseases, cancer, and autoimmune diseases. New software is developed for...
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...
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.
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...
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...
Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article,...
A new assembler called SAUTE is developed for sequence assembly that is based on target enrichment [1].
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...
Latest Comments