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[Tutorial] Installing Rosetta 3.21 on Ubuntu

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Installing Rosetta on Ubuntu
Rosetta is a bioinformatics software for modeling and protein structure analysis [1]. In this articl

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Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

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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

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Software

Installing Autodock4 on MacOS.

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Installing Autodock4 on MacOS
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let&

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Docking

How to install Autodock4 on Ubuntu?

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How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to a

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Software

DS Visualizer: Uses & Applications

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DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and ana

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Software

Protein structure & folding information exploited from remote homologs.

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protein structure & folding prediction using remote homologs
Remote homologs are similar protein structures that share similar functions, but there is no easily

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RNA-seq analysis

Pathonoia- A new tool to detect pathogens in RNA-seq data.

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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

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Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

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AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts

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Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

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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

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Software

How to generate electron density map using Pymol?

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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

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Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

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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,

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Software

How to execute matlab from terminal in Ubuntu (Linux)?

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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

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Software

How to install Kpax on Ubuntu (Linux)?

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How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures [1]. It is currently availab

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Secondary structure

How to run do_dssp command (mkdssp) in Gromacs 2022?

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How to run do_dssp command in Gromacs 2022?
In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command

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Software

Installing SMINA on Ubuntu (Linux).

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Installing SMINA on Ubuntu (Linux)
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy mini

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Software

How to install ClusCo on Ubuntu (Linux)?

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How to install ClusCo on Ubuntu (Linux)?
ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In t

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Software

How to run LigAlign plugin on Pymol?

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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

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Software

How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

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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

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Software

How to install multiple Pymol versions on Ubuntu (Linux)?

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Installing multiple versions of Pymol on Ubuntu
Sometimes we need to access old versions of Pymol [1]. Running some plugins on Pymol is difficult du

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Software

[Tutorial] Installing Pymol on Mac OS.

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installing pymol on mac os
Previously, we provided a tutorial for Pymol installation on Ubuntu. In this article, we are going t

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Software

How to install VMD on Ubuntu?

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

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