Basics of Bioinformatics research from idea to article

Learn the basics of computer aided drug designing and how to publish your first paper from scratch in Bioinformatics.
Basics of Bioinformatics research from idea to article
File Size :
3.06 GB
Total length :
3h 55m


Souvik Chakraborty


Last update




Basics of Bioinformatics research from idea to article

What you’ll learn

Perform gene expression analysis
Create a Protein-protein interaction map and calculate hub genes using Cytoscape
Screening of potential drug targets
ADMET analysis of drugs DruLito and OSIRIS
Perform molecular docking using Autodock Vina
Visualization of the docked complex using Biovia Discovery Studio
Enrichment analysis using EnrichR
Finding microRNAs associated with hub genes using miRNet
Manuscript preparation and using a bibliographic management tool (Zotero will be used)
Select a proper journal (Scopus indexed as well as PubMed indexed) for your first paper.
Uploading a paper to BioRxiv (getting DOI for your first paper)

Basics of Bioinformatics research from idea to article


No prior knowledge of softwares for drug discovery is required as in this course no coding has been used
This course is meant for all the those who have love for life sciences and want to start their research career
This course is meant for all those who are interested in learning computer aided drug designing
This course is meant for those who are interested in learning molecular docking
This course is meant for those who are interested in bioinformatics
This course is meant for all those who are interested in learning bioinformatics (project based approach)


A complete guide to the development of ideas for in-silico research to the publication of a paper – yes this is what you getFrom idea development for research to writing and publishing a paper, yes that is what you get. Learn the basics of data analysis for gene expression analysis, molecular docking, visualization of the docked complex, enrichment analysis, microRNA identification production of publication-quality images, writing a research article properly, and using Zotero – a free reference management tool. In this course, you will be getting a proper idea of how can a set of genes can be used to design drugs and how using molecular docking techniques we can validate our results for the best drug. You will be getting a good idea of ‘drug repurposing’ also after the completion of the hands-on training session associated with this course. No prior knowledge or skills are required to attain this course and this course is deliberately kept straightforward for new learners. In this course, you will get all the necessary skills required to write a research article on your own, guidelines for selecting a proper journal for your manuscript, and also you can extend these research ideas to wet-lab experiments as well.ALL THE BEST:)


Section 1: Introduction

Lecture 1 Intro to the course

Section 2: Study Plan

Lecture 2 Study Plan

Section 3: Data analysis and Manipulation

Lecture 3 Procuring Data

Lecture 4 Data Manipulation

Section 4: Finding the Differentially Expressed Genes (DEGs)

Lecture 5 Creating Venn diagram

Section 5: Identifying Hub genes from Protein-protein interaction network

Lecture 6 Creating PPI and using STRING tool and identifying Hub genes using Cytoscape

Section 6: New way to create Hub gene network using Cytoscape

Lecture 7 Creating hub gene network without using String App

Section 7: Identifying drugs associated with hub genes

Lecture 8 Identification of drugs using Drug gene interaction database (DGIdb)

Section 8: How to draw 3D structures of drugs using Chem Sketch

Lecture 9 Using Chem Sketch to draw 3D structures of ligands

Section 9: Screening of drugs

Lecture 10 Using DruLiTo and OSIRIS for Screening of Drugs

Section 10: Molecular Docking study

Lecture 11 Downloading PDB files of proteins

Lecture 12 UCSF Chimera and AutoDock Vina Installation

Lecture 13 Energy minimization of protein and preparing the protein for molecular docking

Lecture 14 Energy minimization of ligand and preparing it for docking

Lecture 15 Finding pockets for our protein of interest

Lecture 16 fpocket

Lecture 17 Molecular Docking study

Lecture 18 Creating the docked complex file

Lecture 19 Concept of Control drug

Lecture 20 Visualization of the docked complex

Section 11: Producing publication quality images

Lecture 21 Using Adobe Photoshop for producing images for publication

Lecture 22 Using Adobe Photoshop for Producing publication quality images

Section 12: Enrichment analysis

Lecture 23 Enrichment analysis using Enrichr

Section 13: Identification of microRNAs associated with top ten hub genes

Lecture 24 Using miRNet for identification of microRNAs associated with top ten hub genes

Section 14: Writing your first paper

Lecture 25 Anatomy of a research article and selection of correct journal

Lecture 26 Preparing manuscript for journal and using Zotero for reference management

Lecture 27 Uploading your manuscript to BioRxiv

Section 15: Course Conclusion

Lecture 28 Course Conclusion

Anyone interested in any branch of life science,Aspiring researchers,Anyone who wants to know how a drug discovery process looks like,Anyone interested in in-silico research,Anyone who want to learn computer aided drug designing,Anyone interested in learning molecular docking,Anyone interested in bioinformatics

Course Information:

Udemy | English | 3h 55m | 3.06 GB
Created by: Souvik Chakraborty

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