Molecular Docking 2023

Determining Protein-Ligand Interactions Using Molecular Operating Environment (MOE)

What you'll learn

Participants will gain a solid understanding of the fundamental concepts of molecular docking, including ligands, proteins, binding sites, and interactions.

Participants will be able to explain the concept of binding affinities and how they relate to ligand-protein interactions.

Participants will explore various real-world applications of molecular docking in fields like drug discovery and protein engineering.

Participants will learn how to prepare protein and ligand structures for docking simulations.

Participants will be able to set up docking simulations, define binding sites, and configure parameters for docking runs.

Participants will become proficient in using the Molecular Operating Environment (MOE) software for performing molecular docking simulations.

Participants will acquire skills in interpreting docking results, analyzing binding poses, and evaluating ligand-protein interactions.

Participants will understand the limitations of molecular docking methods and when alternative approaches might be more suitable.

Requirements

Participants should have a foundational understanding of biology and chemistry concepts, including molecular structures, atoms, bonds, and basic biochemical processes.

A basic understanding of bioinformatics concepts will be helpful.

Participants should be comfortable using computers and have basic knowledge of software applications, as the course involves using molecular docking software.

A basic understanding of chemical principles, such as molecular geometry, molecular forces, and bonding, will be beneficial.

Basic knowledge of biological concepts, such as protein structure, enzymatic function, and binding interactions, will provide a foundation for understanding the relevance of docking simulations.

A foundational understanding of molecular biology and biochemistry concepts will enhance participants' ability to comprehend the biological context of docking simulations.

Previous exposure to computational tools or software will be advantageous, as participants will be working with molecular docking software.

The course is designed for beginners and contains more foundational content and explanations. However, basic knowledge of biology, chemistry, biochemistry, molecular biology, and bioinformatics is required.

Description

This course offers a comprehensive exploration of the intricate world of molecular docking, commencing with an in-depth overview of key terminologies and step-by-step docking procedures. Through engaging visuals and interactive content, participants will master the essential building blocks required to conduct successful molecular docking studies. Central to the course is an immersive exploration of molecular docking using the Molecular Operating Environment (MOE), a prominent software platform in the field. Participants will embark on a guided journey through each phase of docking, backed by captivating visuals and illustrative videos. They will not only grasp the theoretical underpinnings but also gain hands-on experience in executing docking simulations using MOE, making the transition from theory to practice seamless. The course ensures a holistic learning experience, catering to various learning styles through a balanced blend of comprehensive reading materials and insightful video content.The course also delves into the inherent limitations of molecular docking, providing participants with a realistic perspective on the technique's strengths and boundaries. As a culmination of their learning journey, participants will have the opportunity to assess their newfound expertise through two practice tests, ensuring their readiness to apply the acquired knowledge. Additionally, an assignment challenges participants to apply their skills in a practical context, reinforcing their ability to execute molecular docking studies effectively. Thus, through engaging reading materials, insightful videos, practice tests, and real-world assignments, this course provides an unparalleled opportunity to enhance expertise in molecular docking.

Overview

Section 1: Introduction to the Course

Lecture 1 Course Outline

Section 2: Theoretical Framework for Molecular Docking

Lecture 2 Introduction to Molecular Docking

Lecture 3 Basic Terminologies

Lecture 4 Key Steps in Molecular Docking

Section 3: Mid Term

Section 4: Performing Molecular Docking Using MOE

Lecture 5 Target Selection and Preparation (Part 1)

Lecture 6 Target Selection and Preparation (Part 2)

Lecture 7 Ligand Selection and Preparation

Lecture 8 Running Docking Simulation

Lecture 9 Analyzing Docking Results

Lecture 10 Visualizing 2D Interactions Using BIOVIA Discovery Studio

Lecture 11 Limitations of Molecular Docking

Section 5: Final Term

Biology and Chemistry Students,Researchers and Scientists,Pharmaceutical Industry Professionals,Bioinformaticians,Educators and Instructors,Researchers in Structural Biology,Graduates of Introductory Bioinformatics Courses,Students of Biochemistry and Molecular Biology,Anyone Interested in Drug Discovery,Anyone Interested in Molecular Docking