SARS-CoV-2 Spike Glycoprotein Modelling and Docking Studies.

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PyMOL Visualisation of Protein & Drug Docking Results

The stages that follow the design or identification of a new drug are both costly and time-consuming. The entire process of drug development can take from 12 to 15 years and cost billions of dollars, but in-silico molecular docking studies have been seen to both speed up the discovery rate and reduce (although not eliminate!) the need for expensive lab work.

Hence molecular docking studies are very crucial in speeding up drug discovery and screening processes in times such as the current COVID-19 pandemic.

In order to educate the mass about docking procedure I have created a simple course!

By the end of this project, you will construct a 3D structure of a SARS-CoV-2 protein sequence using homology modeling and perform molecular docking of drugs against this protein molecule and infer protein-drug interaction which is essential in drug screening and discovery phase. …


Setting up protein-drug docking environment on windows subsystem for Linux (WSL 2).

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Photo by National Cancer Institute on Unsplash

Protein-docking is a molecular modeling problem which aims to predict, with computer science algorithms and techniques, the mutual orientation and position of two molecules forming a complex. One of the molecules is a protein, the other could be another protein, a nucleic acid chain or a smaller molecule.

virtual screening is used to identify small molecules that are most likely to bind to a target protein. There is various software available for virtual screening including GOLD and GLIDE. Autodock Vina which is a freely accessible software and provides good results can also be used for screening various ligands.

AutoDock Vina is one of the most popular software in Bioinformatics, known for the molecular docking simulations. In this small tutorial, we will learn how to install AutoDock Vina on Ubuntu. Its installation on Ubuntu may be a tedious process, especially for the beginners due to the unfamiliarity of the Linux commands. It is expected to work on any version of Ubuntu/ WSL 2 but make sure whether your system supports the 32- bit or 64- bit version. If you face any problem, then feel free to ask.You need a good Internet connection as you will have to download different files. We need to download the following software to install AutoDock…


Find a job that aligns with your skills and interests by web scraping.

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Photo by Kevin Bhagat on Unsplash

With so many factors involved in making a career move, it’s hard to know where to start or know what decision is the right one (Also credits to the ongoing COVID-19 pandemic to have added the “extra” right before the word “confusion”).

I’m thinking about my next job.

Where do you think I should work next?

Which companies do you think are interesting?

I think it’s time for me to consider the next phase in my career.

I’ve heard the above statements a lot over the years. Even if you’re at the very beginning of your next-move exploration, you already have a list of goals you want to achieve in your head. …


RStudio server on Windows WSL2 which now supports GPU compute.

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Photo by Pietro Mattia on Unsplash

I present to you a super-easy guide for setting up and running RStudio Server for Ubuntu 20 on Windows 10. This is useful if you want to run R for Linux (e.g., due to its faster computation and better parallelization or simply to do cross-platform development) while on a Windows machine.

At Build 2020 Microsoft announced support for GPU compute on Windows Subsystem for Linux 2. I mean How cool is that?

This article explains how to set up RStudio Server on Windows platform.

Prerequisite

Using the enhanced WSL (version 2) for setting up RStudio Server is recommended, which requires Windows 10 (Version 2004; Build 19041 or higher). …


Database of cool names for your next inventions and business ventures ?

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Photo by ray rui on Unsplash

What is sci-fi A.K.A. science fiction ?

Science fiction, often called “sci-fi,” is a genre of fiction literature whose content is imaginative, but based in science. It relies heavily on scientific facts, theories, and principles as support for its settings, characters, themes, and plot-lines, which is what makes it different from fantasy.

One cannot distinguish between reality and sci-fi in this dawn of A.I. technology.

So, while the storylines and elements of science fiction stories are imaginary, they are usually possible according to science — or at least plausible.

So what’s the big deal about sci-fi ?

Other than building a smart program to search entire search-engine and stack-overflow to debug it’s own errors you ask? …


Add a little extra something to your CV and some great talking point in interviews.

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Unsplash: United Nations COVID-19 Response

The coronavirus pandemic has increased interest in online education and brought MOOCs back into the spotlight. As the outbreak continues to evolve, we need to update ourselves with the resources and skills to best reflect the changing context in order to have a competitive edge over our peers.

Online courses are a great way to boost your employment prospects: they add a little extra something to your CV and are a great talking point in interviews, as well as being a great way to spend your free time. …


Improve your resume with the first pure Bioinformatics hands-on project with python.

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3D Coronavirus Blender Model

Why do we need to Visualize Proteins ?

In the fields of Bioinformatics, Health and Medical Technology & Biotechnology, there is now a widespread need for visualization tools to present the 3D structure of proteins.

There are only a few examples of protein function. A remarkable fact is that all tasks they can perform are based on a common principle, the twenty amino acids that can form a protein. That is the reason why studying proteins, their composition, structure, dynamics and function, is so important.

We must understand how these molecules fold, how they assemble into complexes, how they function if we wish to answer questions such as why we have cancer, why we grow old, why we get sick, how can we find cures for many diseases, why life as we know it has evolved in this way and on this planet and not anywhere else, at least for the moment. All proteins functions are dependent on their structure, which, in turn, depends on physical and chemical parameters.


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Photo by rupixen.com on Unsplash

This article is dedicated to all my fellow Indian Authors & Bloggers on Medium.

The struggle has come to an end , for all the writers out there who have dug the deepest corners of the web in search for a way to make a living out of writing.

Yes, you can earn from blogging , Yes from Medium, Yes even if you are from India or Brazil.

Let me show you how; but before that let’s understand the current scenario :

Stripe

  • Offers a preview mode for India, where you can create an account but with limited features with it’s own share of restrictions


Accelerate ML & Data Science development

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Photo by Andy Kelly on Unsplash

Most Data Science, Machine learning projects start with importing endless number of modules and packages, Writing the same imports over and over again is below your capacity. There are several problems with this. Admittedly, they are small but they add up over time.

Missing imports disrupt the natural flow of your work. Sometimes, you may even need to look up the exact import statements, like import matplotlib.pyplot as plt or from sklearn.ensemble import GradientBoostingRegressor.

What if you could just focus on using the libraries?

Source: Giphy

Content Overview

  1. What is pyforest
  2. Installing pyforest
  3. Using pyforest
  4. Understanding with simple Python code

Before we start let’s have a quick look at this beautiful…


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Photo by Joshua J. Cotten on Unsplash

The route into the web or application development world can seem obfuscated at times — there’s no clear path since there are multiple programming languages, hundred of frameworks, and thousands of libraries. Consequently, it can be hard to know which languages to learn and in what order. Once you have answered this question, the next step to take is typically to spend a lot of time in front of a text editor, setting up an environment and manipulating it as you need. By the time you are done going through your system configuration, compatibility & git setup, your motivation to work gets postponed and your patience has worn thin. This is a frustrating place to find yourself. …

About

Bhagesh Hunakunti

Pursuing Masters in Bioinformatics, Digital artist and content creator. Contact: https://linktr.ee/BhageshCodebeast

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