Software

A collection of published articles on different bioinformatics software.

Latest Software News

Genozip- a new compression tool for VCF files

Variant Call Format (VCF) is a text file format used to store…

Tariq Abdullah

Installing CHARMM on Ubuntu

CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that…

Tariq Abdullah

Tutorial: Basic protein structure modeling using MODELLER

SALI MODELLER is one of the most widely used command-line bioinformatics software…

Dr. Muniba Faiza

Installing PyMol on Ubuntu

PyMol is a molecular visualization software that is freely available for education-use-only…

Tariq Abdullah

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…

Tariq Abdullah

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…

Dr. Muniba Faiza

How to perform graph-based clustering of peptide/protein sequences using MCL?

Markov Cluster Algorithm (MCL) is a clustering algorithm that clusters networks .…

Tariq Abdullah

Tutorial: A quick MD simulation using NAMD and VMD

Molecular dynamics (MD) simulation has become an important methodology in research covering…

Dr. Muniba Faiza

Tutorial: MD simulation output analysis of protein using GROMACS

Molecular dynamics (MD) simulation is an important step in studying the dynamics…

Tariq Abdullah

Video tutorial: Installing GROMACS on Ubuntu

This is a video tutorial of our existing article on GROMACS (Abraham,…

Dr. Muniba Faiza

Beginner’s Guide for Docking using Autodock Vina

We have compiled all articles on docking into a Special Issue. This…

Bioinformatics Review

How to perform virtual screening using Autodock Vina?

Virtual screening is used to identify small molecules that are most likely…

Dr. Muniba Faiza

Protein-ligand interaction analysis using LigPlot+

In our last article, we explained the installation of LigPlot+ on Ubuntu.…

Tariq Abdullah

Installation of LigPlot+ on Ubuntu

LigPlot+ is a bioinformatics software to visually analyze the protein-ligand interactions in…

Dr. Muniba Faiza

How to install DeepView-Swiss PDB Viewer on Linux?

DeepView (Swiss-PDB Viewer) is used to analyze multiple proteins simultaneously. Protein structure…

Tariq Abdullah

MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers

I have received several e-mails from researchers and students alike regarding installing…

Tariq Abdullah

Tutorial: Molecular dynamics (MD) simulation using Gromacs

Gromacs is one of the most widely used software for molecular dynamics…

Dr. Muniba Faiza

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…

Tariq Abdullah

Vina output analysis using Discovery Studio visualizer

The discovery studio (DS) visualizer offers several features for analyzing docking results.…

Dr. Muniba Faiza

Installing and executing ProtTest3 on Ubuntu

Prottest3 is a software which is used to select a best-fit amino…

Dr. Muniba Faiza