Open Babel is an open-source chemical toolbox for molecular modeling and cheminformatics tasks. It is a versatile conversion tool that supports various chemical file formats, enabling...
DS Visualizer is a comprehensive, free molecular modeling and visualization tool designed by BIOVIA, part of Dassault Systèmes [1]. It enables researchers to visualize and analyze...
![[Tutorial] Installing HTSlib on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2024/08/03204655/htslib.jpg)
![[Tutorial] Installing HTSlib on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2024/08/03204655/htslib-400x240.jpg)
![[Tutorial] Installing HTSlib on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2024/08/03204655/htslib-80x80.jpg)
HTSlib is an open-source C library designed for handling high-throughput sequencing (HTS) data [1]. It provides the underlying functionality for manipulating various file formats commonly used...
CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage...
Interactive Genome Viewer (IGV) is an interactive tool to visualize genomic data [1]. In this article, we are installing IGV and tools on Ubuntu desktop.
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/12/01184130/viamd.jpg)
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/12/01184130/viamd-400x240.jpg)
![[Tutorial] Installing VIAMD on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/12/01184130/viamd-80x80.jpg)
Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing...
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock.jpg)
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock-400x240.jpg)
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock-80x80.jpg)
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...
