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jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and...
GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA...
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article....
PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on...
Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going...
ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux).
Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult due to Python incompatibility. New Pymol versions require Python...
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...
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...
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...
Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this article, we are going to install this software on Ubuntu.
PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It performs molecular docking of any two types of molecules including proteins,...
There are commonly used alignment programs such as muscle, blast, clustalx, and so on, that can be easily installed from the repository. In this article, we...
CDK stands for chemistry development kit [1]. This is an open source kit for cheminformatics consisting of modular JAVA libraries. In this article, we will install...
Anaconda is an open-source toolkit that is useful in programming and machine learning using Python/R [1]. In this article, we are going to install Anaconda3 on...
Pycharm [1] is an integrated development environment (IDE) for developers. It combines Python developer tools and provides an easy graphical user interface. In this article, we...
