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…
Sequence search against a set of local sequences (local database) using phmmer
PHMMER is a sequence analysis tool used for protein sequences (http://hmmer.org; version…
Vina output analysis using Discovery Studio visualizer
The discovery studio (DS) visualizer offers several features for analyzing docking results.…
Installing and executing ProtTest3 on Ubuntu
Prottest3 is a software which is used to select a best-fit amino…