Software
Installing Anaconda3 on Ubuntu (Linux)
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 Ubuntu (Linux).
Preparing system
Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:
$ sudo apt-get update
$ sudo apt-get upgrade
Installing prerequisites
You need to install the following libraries to run Anaconda on your system. Paste the following command in the terminal.
$ sudo apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6
Downloading Anaconda
At first, change to the directory where you want to download the software. Let’s say ‘Downloads‘.
$ cd Downloads/
You can either manually download the latest version of the Anaconda installer from here or use the following command.
$ wget https://repo.anaconda.com/archive/Anaconda3-2021.05-Linux-x86_64.sh
It will take a moment to finish downloading.
Installing Anaconda
Let’s first verify the integrity of the installer using the following command.
$ sha256sum Anaconda3-2021.05-Linux-x86_64.sh
It should display something like this:
45c851b7497cc14d5ca060064394569f724b67d9b5f98a926ed49b834a6bb73a Anaconda3-2021.05-Linux-x86_64.sh
Now, let’s run the Anaconda script.
$ bash Anaconda3-2021.05-Linux-x86_64.sh
It will show you a license. In the end, type yes to agree to the license. After the license agreement, you will be prompted to select the installation location. Select appropriately and let the installation process complete.
Now, activate the installation using the following command.
$ source ~/.bashrc
You can check the installation by typing $ conda list
command. It will list all the packages available through Anaconda.
Setting up Anaconda environment
Let,s create a Python3 environment as my_env.
$ conda create --name my_env python=3
Now, activate the new environment as shown below.
$ conda activate my_env
Now, Anaconda has been installed successfully on your system.
References
- Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. <https://anaconda.com>.
MD Simulation
[Tutorial] Installing VIAMD on Ubuntu (Linux).
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 it on Ubuntu (Linux).
Docking
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
Docking
How to install the DockingPie plugin on PyMOL?
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 using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
Software
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
Software
How to generate topology from SMILES for MD Simulation?
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Software
[Tutorial] Installing jdock on Ubuntu (Linux).
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 the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).
Software
How to upgrade cmake on Ubuntu (Linux)?
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Software
How to install GMXPBSA on Ubuntu (Linux)?
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 version 2.1.2 on Ubuntu (Linux).
Docking
[Tutorial] Installing Pyrx on Windows.
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. (more…)
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
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 frequently occurring during GROMACS installation.
Software
Installing Autodock4 on MacOS.
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
Docking
How to install Autodock4 on Ubuntu?
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. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
Software
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.
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Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
RNA-seq analysis
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
How to generate electron density map using Pymol?
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
Software
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
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 Ubuntu. (more…)
Software
How to execute matlab from terminal in Ubuntu (Linux)?
While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
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