Plugin to visualize CASTp results in PyMOL
CASTp (Computed Atlas of Surface Topography of proteins) server is used to…
Prepare receptor and ligand files for docking using Python scripts
Docking software such as Autodock4 and Autodock Vina require input receptor and…
Genozip- a new compression tool for VCF files
Variant Call Format (VCF) is a text file format used to store…
Installing CHARMM on Ubuntu
CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that…
Tutorial: Basic protein structure modeling using MODELLER
SALI MODELLER is one of the most widely used command-line bioinformatics software…
Installing PyMol on Ubuntu
PyMol is a molecular visualization software that is freely available for education-use-only…
Homology search against a local dataset using NCBI-BLAST+ command-line tool
NCBI-BLAST+ command-line tool offers multiple functions to be performed on a large…
How to use Clustal Omega and MUSCLE command-line tools for multiple sequence alignment?
Clustal Omega and MUSCLE are bioinformatics tools that are used for multiple…
How to perform graph-based clustering of peptide/protein sequences using MCL?
Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks .…
Tutorial: A quick MD simulation using NAMD and VMD
Molecular dynamics (MD) simulation has become an important methodology in research covering…
Tutorial: MD simulation output analysis of protein using GROMACS
Molecular dynamics (MD) simulation is an important step in studying the dynamics…
Video tutorial: Installing GROMACS on Ubuntu
This is a video tutorial of our existing article on GROMACS (Abraham,…
Beginner’s Guide for Docking using Autodock Vina
We have compiled all articles on docking into a Special Issue. This…
How to perform virtual screening using Autodock Vina?
Virtual screening is used to identify small molecules that are most likely…
Protein-ligand interaction analysis using LigPlot+
In our last article, we explained the installation of LigPlot+ on Ubuntu.…
Installation of LigPlot+ on Ubuntu
LigPlot+ is a bioinformatics software to visually analyze the protein-ligand interactions in…
How to install DeepView-Swiss PDB Viewer on Linux?
DeepView (Swiss-PDB Viewer) is used to analyze multiple proteins simultaneously. Protein structure…
MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers
I have received several e-mails from researchers and students alike regarding installing…
Tutorial: Molecular dynamics (MD) simulation using Gromacs
Gromacs is one of the most widely used software for molecular dynamics…
Installing and executing ProtTest3 on Ubuntu
Prottest3 is a software which is used to select a best-fit amino…