Software
[Tutorial] Installing Rosetta 3.21 on Ubuntu

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 sa
Software
Installing Autodock4 on MacOS.

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let&
Docking
How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to a
Software
DS Visualizer: Uses & Applications

Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and ana
Software
Protein structure & folding information exploited from remote homologs.

Remote homologs are similar protein structures that share similar functions, but there is no easily
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
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.

AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calcu
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 ar
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,
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 f
Software
How to install Kpax on Ubuntu (Linux)?

Kpax is a bioinformatics program to search and align protein structures [1]. It is currently availab
Secondary structure
How to run do_dssp command (mkdssp) in Gromacs 2022?

In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command
Software
Installing SMINA on Ubuntu (Linux).

SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy mini
Software
How to install ClusCo on Ubuntu (Linux)?

ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In t
Software
How to run LigAlign plugin on Pymol?

Running a plugin on an old version of Pymol [1] can give you multiple errors that are not easy to tr
Software
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. For example, if you try t
Software
How to install multiple Pymol versions on Ubuntu (Linux)?

Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult du
Software
[Tutorial] Installing Pymol on Mac OS.

Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going t
Software
How to install VMD on Ubuntu?

In this article, we are going to install VMD [1] on Ubuntu. (more…)
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