How to generate topology from SMILES for MD Simulation?
If you need to generate the topology of molecules using their SMILES,…
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://bioinformaticsreview.com/wp-content/uploads/2023/05/jdock.jpg)
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . It has the same…
How to install GMXPBSA on Ubuntu (Linux)?
GMXPBSA is a tool to calculate binding free energy . It is…
![[Tutorial] Installing Pyrx on Windows.](https://bioinformaticsreview.com/wp-content/uploads/2023/04/pyrx-3.jpg)
[Tutorial] Installing Pyrx on Windows.
Pyrx is another virtual screening software that also offers to perform docking…
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS with GPU can be trivial. Previously, we have provided a…
Installing Autodock4 on MacOS.
Previously, we installed the Autodock suite on Ubuntu. Visit this article for…
How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules . Recently, Autodock-GPU is…
DS Visualizer: Uses & Applications
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing,…
Protein structure & folding information exploited from remote homologs.
Remote homologs are similar protein structures that share similar functions, but there…
Pathonoia- A new tool to detect pathogens in RNA-seq data.
Detecting viruses and bacteria in RNA-seq data with less false positive rate…
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . Though…
How to calculate binding pocket volume using PyVol plugin in PyMol?
Previously, we provided a tutorial for PyVol plugin installation. In this article,…
How to generate electron density map using Pymol?
Electron density maps are available for most of the protein structures in…
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
PyVOL is an excellent plugin of Pymol for pocket visualization of proteins.…
How to download FASTA sequences from PDB for multiple structures?
In this article, we are going to download FASTA sequences for multiple…
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures .…
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , there are some issues…
Installing SMINA on Ubuntu (Linux).
SMINA is a fork of AutoDock Vina supporting better scoring function and…
How to install ClusCo on Ubuntu (Linux)?
ClusCo is a bioinformatics software to perform clustering and comparison of protein…
