ProteStAr is a bioinformatics tool to compress protein structure files [1]. It compresses PDB/CIF files and supplementary PAE files. The compression is lossless. However, users are...
Understanding the relationship between genes and proteins is crucial for elucidating biological processes, and disease mechanisms, and developing targeted therapies. A new tool developed by Yang...
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...
In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It...
Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and...
Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py...
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] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1.jpg)
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1-400x240.jpg)
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1-80x80.jpg)
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock...
The CASTp server allows you to predict the binding sites in a protein [1]. In this article, we will predict binding sites in a protein using...
This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
![[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...
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3-400x240.jpg)
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3-80x80.jpg)
Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows.
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error...
![[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)
Latest Comments