Introduction to Molecular Modeling in Drug Discovery

Issued by: Schrödinger
Completed on: April 28th, 2021

Course Overview:
This course provides a foundational understanding of computational molecular modeling tools and their application in drug discovery. It is designed for scientists who wish to learn industry-standard methods for small molecule design. The curriculum offers hands-on experience with Schrödinger’s Maestro and LiveDesign platforms, covering key workflows from protein preparation and ligand docking to collaborative design in a real-world case study.

Key Skills Acquired:

• Molecular Modeling Fundamentals: Gained a strong understanding of the theory and practical application of computational tools in drug discovery projects.
• Maestro Proficiency: Developed hands-on skills in using the Maestro graphical user interface for tasks such as modifying small molecules, viewing protein-ligand interactions, and preparing structures for modeling.
• Structure & Ligand-Based Design: Learned best practices for protein and ligand preparation (LigPrep), ligand docking for structure-based virtual screening, and shape-based screening for ligand-based design.
• Collaborative Drug Design: Utilized the LiveDesign platform to organize data, apply workflows for multi-parameter optimization, and ideate novel compounds in a collaborative environment.
• Practical Application: Completed an independent case study on designing novel VEGFR2 inhibitors, demonstrating mastery of the course content from hit analysis to analog ideation.

Curriculum: The course was structured into seven modules, covering:

1. Introduction to Molecular Modeling: The value and application of modeling in case studies.
2. Maestro Fundamentals: Core skills for navigating the interface and modifying molecules.
3. Protein-Ligand Interactions: Visualization, ligand preparation, and alignment.
4. Structure-Based Virtual Screening: Protein preparation, grid generation, and ligand docking.
5. Ligand-Based Virtual Screening: Shape-based screening methods.
6. LiveDesign Workflows: Collaborative data organization and ideation.
7. VEGFR2 Case Study: A final project applying all learned skills to a real-world target.

This course provided practical, hands-on training in the essential workflows for modern computational drug discovery.

You can view the certificate here.