Basics of Computer Aided Drug Discovery Part-I

Name: Basics of Computer Aided Drug Discovery Part-I
Rating: 4.0 (159 reviews)

Basics of Computer Aided Drug Discovery

Created byHussain Basha Syed

Last updated 9/2021

English

What you'll learn

Introduction to Computer Aided Drug Discovery.
Introduction to databases like PDB, PubChem and ZINC database.
How to visualize protein and ligands in Biovia Discovery Studio and MGLtools.
How to prepare files for docking studies.
How to execute molecular docking.
How to analyze the docking output results.
How to generate publication quality figures from the docking output.

Course content

9 sections • 20 lectures • 2h 32m total length

Introduction to the course2:45
Learn the basics of computer aided drug discovery with computation, from the drug discovery pipeline to molecular docking, docking types, file preparation, result analysis, and publication-ready visualizations.

Introduction to visualization of protein in Biovia Discovery studio9:09
Visualize the protein in Biovia Discovery Studio with dynamic display styles, residue and atom details, multiple representations, and color and surface options to reveal structure and function.
Introduction to visualization of Ligand in Biovia Discovery studio2:21
Explore visualizing a ligand in Biovia Discovery Studio by opening the compound, viewing data tables, atomic and residue information, bonds and lengths, and adjusting display styles and color by element.

Preparation of ligand5:04
Preparation of protein receptor4:02
Preparation of autogrid parameter file8:00
Prepare the grid parameter file (GPF) by selecting the macromolecule, setting grid boundaries, and saving the Autodock parameter library and affinity maps.
Preparation of autodock parameter file2:42
Prepare a docking parameter file for autodock using a Lamarckian genetic algorithm, set ligand details and center coordinates, generate random population, use default medium evaluation, save as protein_ligand.dpf.
Visualizing autodock parameter file1:24
Visualize and edit the autodock dpf to review atom types, affinity maps, electrostatic and desolution maps, move ligand, and torsional degrees of freedom, with ten GA runs and clustering analysis.
Executing autogrid parameter file4:23
Executing autodock parameter file1:25
Execute the docking parameter file by launching autodock with the DPF file after completing auto grid, run the autodock in background, and note warnings while awaiting docking completion.

Requirements

Basic knowledge of computers applications and Internet access.

Description

A perfect course for Bachelors / Masters / PhD students who are getting started into Drug Discovery research. This course is specially designed keeping in view of beginner level knowledge on computational drug discovery applications for science students. By the end of this course participants will be equipped with the basic knowledge required to navigate their drug discovery project making use of the biological databases and computational tools.

Who this course is for:

Bachelors or Masters degree or PhD scholar of Pharmaceutical sciences, Biochemistry, Biotechnology, Chemistry or related who are into drug discovery research will benefit most of this course.

Basics of Computer Aided Drug Discovery Part-I

What you'll learn

Explore related topics

Course content

Introduction to the course1 lecture • 3min

Introduction to Computer Aided Drug Discovery1 lecture • 10min

Introduction to Biological databases3 lectures • 44min

Download and Installation of MGLtools and Biovia Discovery Studio2 lectures • 5min

Introduction to visualization of protein and ligand in Biovia Discovery studio2 lectures • 12min

Introduction to visualization of protein and ligand in MGLtools1 lecture • 9min

Rationale behind molecular docking application and its types1 lecture • 16min

Introduction to molecular docking using Autodock7 lectures • 27min

Analyzing molecular docking result output from Autodock2 lectures • 28min

Requirements

Description

Who this course is for: