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Answer for What is the scope of Bioinformatics in India?

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In India, Bioinformatics has high hopes as it is still in nascent field. The growth of this field is also dependent on growth of Biotechnology. 
There are a lot of big bioinformatics companies in India that hire bioinformaticians. Some of them include Accelerys, Jubilant etc. 
Complete list can be found by clicking here.

in 2010-11, Indian bioinformatics market was valued at US$58 Million While it was expeccted to grow by 25% in 2015.
 
In a market that require a large number of trained professionals, Bioinformatics can be a good choice.
 

The Team at Bioinformatics Review includes top notch bioinformaticians and scientists from across the world. Visit our Team page to know more.

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Software

[Tutorial] How to install 3Dmapper on Ubuntu (Linux)?

Dr. Muniba Faiza

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Installing 3Dmapper on Ubuntu (Linux).

Understanding the relationship between genes and proteins is crucial for elucidating biological processes, and disease mechanisms, and developing targeted therapies. A new tool developed by Yang et. al., [1], provides a better solution to map annotated positions and variants to protein structures automatically. 3Dmapper is a stand-alone tool based on R and Python programming languages that map annotated genomic variants or positions to protein structures [1]. In this article, we will install 3Dmapper on Ubuntu (Linux).

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Software

CMake installation and upgrade: What worked & what didn’t?!

Dr. Muniba Faiza

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CMake installation and upgrade: What worked & what didn’t?!

CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage the build process of software tools and pipelines used for data analysis, algorithm implementation, and other computational tasks. However, managing the versions of CMake or upgrading it on Ubuntu (Linux) can be a trivial task for beginners. In this article, we provide methods for installing and upgrading CMake on Ubuntu.

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Bioinformatics Programming

Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.

Dr. Muniba Faiza

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In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as a crucial tool for understanding the behavior of molecules and biomolecules over time. It is difficult to understand and plot a meaningful FEL and then extract the time frames at which the plot shows minima. In this article, we introduce a new Python package (Free_Energy_Landscape-MD) to generate an FEL based on principal component analysis (PCA) from MD simulation done by GROMACS [1].

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Molecular dynamics

How to generate PSF file for MD simulation using NAMD & VMD?

Dr. Muniba Faiza

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Protein structure file (PSF) contains topology information and is required for molecular dynamics (MD) simulation in NAMD [1] and VMD [2]. In this tutorial, we will generate a PSF file of a simple protein using NAMD and VMD.

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Bioinformatics News

VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

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Bioinformatics Programming

vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Dr. Muniba Faiza

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vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Analyzing the results of virtual screening (VS) performed with Autodock Vina [1] can be challenging when done manually. In earlier instances, we supplied two scripts, namely vs_analysis.py [2,3] and vs_analysis_compounds.py [4]. This time, we have developed a new Python script to simplify the analysis of VS results.

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Software

How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Dr. Muniba Faiza

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How to install Interactive Genome Viewer (IGV) & tools on Ubuntu?

Interactive Genome Viewer (IGV) is an interactive tool to visualize genomic data [1]. In this article, we are installing IGV and tools on Ubuntu desktop.

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MD Simulation

[Tutorial] Installing VIAMD on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing VIAMD on Ubuntu (Linux).

Visual Interactive Analysis of Molecular Dynamics (VIAMD) is a tool that allows the interactive analysis of molecular dynamics simulations [1]. In this article, we are installing it on Ubuntu (Linux).

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Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

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Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

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How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

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Structural Bioinformatics

How to predict binding pocket/site using CASTp server?

Dr. Muniba Faiza

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Binding site prediction using CASTp server.

The CASTp server allows you to predict the binding sites in a protein [1]. In this article, we will predict binding sites in a protein using the same.

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Bioinformatics News

Proteins shape analyses reveal novel forms and connections.

Dr. Muniba Faiza

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Protein shape analyses reveal novel forms and connections.

A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

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MD Simulation

Energy minimization and equilibration of simple protein using NAMD & VMD.

Dr. Muniba Faiza

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Energy minimization and equilibration of simple protein using NAMD & VMD.

In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.

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MD Simulation

Generating topology of molecule for AMBER forcefield for GROMACS.

Dr. Muniba Faiza

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Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.

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Tips & Tricks

Common mistakes made during computational docking.

Dr. Muniba Faiza

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Common mistakes made during docking.

Computational docking is not a trivial task once we avoid making some mistakes. In this section, let’s learn about some important points that we should keep in mind while performing computational docking.

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Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

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Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

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Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

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How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.

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Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

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Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to upgrade cmake on Ubuntu/Linux?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)

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Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to install GMXPBSA on Ubuntu (Linux)?

GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).

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