Introduction to Molecular Modeling in Drug Discovery

A Schrödinger Online Course

Schrödinger's online course, Introduction to Molecular Modeling in Drug Discovery will show how industry-leading computational molecular modeling tools are used to aid in drug discovery and design. On average, the course takes about 25 hours over a span of 5 weeks to complete. In addition to utilizing modern techniques such as active learning and multimodal teaching, this course will also provide a chance to work hands-on with Schrödinger's Maestro and LiveDesign.

Session DateRegistration and Payment Deadline
February 7th, 2023  - March 15th, 2023 January 31st, 2023 
April 4th, 2023  - May 10th, 2023March 28th, 2023
May 23rd, 2023 - June 28th, 2023May 16th, 2023


Schrödinger’s online course does not require any books, access to specific journals (though many references are included for those who do have journal access). Access to relevant Schrödinger software is included during the course. 

Course Requirements

Access to a computer with a high-speed internet connection (8 Mbps or better). You can check your internet speed here.


Recommended Materials

Use of a 3-button mouse with a scroll wheel will allow participants to easily follow along with the course videos. Additionally, an external monitor is helpful if one is available.

Finally, as a background level of knowledge, participants should:

  • Be comfortable with common organic chemistry terms, 
  • Have some familiarity with the drug discovery pipeline, 
  • Be able to work on a computer with reliable high-speed internet, and have a working knowledge of protein function. 
  • Be familiar with the concepts of protein structure, compound potency, molecular mass, and pKa. 
    • Participants that are not familiar with protein structure can supplement their knowledge through lectures that are offered by Khan Academy
  • Participants should also be familiar with cellular components and the role of proteins in cells. 
  • An understanding of the role of kinases, receptors, and other enzymes is valuable, but not critical.



The course fee is $515 for non-student participants and $380 for student participants. Groups of 5 or more can get a $50 discount per person.



Broken up into 7 modules, this course is entirely self-paced. It will take approximately 25 hours for someone new to computational modeling to complete (actual time may vary depending on experience). The modules can be done on your own schedule.

Module 1 - Applying Molecular Modeling to Drug Discovery

  • Course Syllabus
  • Pretest for Molecular Modeling in Drug Discovery
  • Video: Molecular Modeling Concepts in Drug Discovery
  • End of Module Exercises


Module 2 - Creating Computational Molecules with Maestro

  • Video: Bring Molecules into Maestro
  • Video: Create and Modify Small Molecules
  • End of Module Exercises


Module 3 - Viewing Protein-Ligand Interactions

  • Video: Bring Proteins into Maestro
  • Read: Medicinal Chemists Guide to Molecular Interactions
  • End of Module Exercises


Module 4 - Modeling Protein-Ligand Poses in Hit Identification and Optimization

  • Video: Modeling Protein-Ligand Poses for Hit Identification
  • Video: Find New Protein-Ligand Poses with Docking
  • Cheat Sheet: Pose Inspection
  • Best Practices Video: Enumerating with the Ligand Designer
  • End of Module Exercises


Module 5 - Ligand-Based Virtual Screening in Preparation for SAR

  • Video: Ligand-Based Screening Methods
  • Tutorial: High-Throughput Ligand-Based Virtual Screens
  • Cheat Sheets: Computational Drug Design
  • End of Module Exercises


Module 6 - Combining Modeling and Experimental Data for SAR Development

  • Video: Organize Data and Collaborate Effectively in Drug Design
  • Video: Workflows for Collaborative Drug Discovery
  • Tutorial: Ideation for Drug Discovery Projects
  • End of Module Exercises


Module 7 - Drug Discovery Case Study on VEGFR2

  • Video: Background on Kinase Structure and Activity
  • Case Study: VEGFR2 Kinase Inhibitors
  • Video: Summary of Short Course and Introduction to Advanced Topics


Get Started!

Ready to start learning? Simply click the register button below to get started. Please note a Schrödinger Web Account is required to access the registration page. If you don't already have a web account you can request one here. For additional information about the course, please email



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