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Online Course: Introduction to Molecular Modeling for Drug Discovery



Online Course: Introduction to Molecular Modeling for Drug Discovery

Monday, October 4, 2021, 12:00 AM - Wednesday, November 17, 2021, 11:59 PM EST

Online Course

Presented By

Science Alliance

Schrodinger LLC


Please note that the fee is $475 for non-students and $350 for students. On average the course takes about 25 hours over a span of 5 weeks to complete.

Users will need to create an account on

***Registration Closes September, 29th at 8PM***

Are you interested in enhancing your understanding of Drug Discovery sitting in the comfort of your home as you work remotely?

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 and how to incorporate these tools into your research project.

Whether you are looking for professional development or expanded skills for your CV, this course will provide practical applications of computational modeling using active learning strategies and multiple types of content. At the end of the course, you will have a chance to apply the concepts you've learned to a VEGFR2 case study in new cancer treatments using cutting-edge technology.

Upon verified completion of the course participants will receive a certificate of completion and a Schrödinger: Molecular Modeling in Drug Discovery Badge

Course Outline:

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

Course Requirements

Access to a computer with a high-speed internet connection (8 Mbps or better). We also recommend using a mouse, but this is not required.


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), or access to Schrödinger software. 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. Participants should 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.

If you have any questions please email

In order to remain compliant with the Electronic Code of Federal Regulations (eCFR), Schrödinger is not allowed to grant software access to people geographically located in countries subject to U.S. sanctions.

Frequently Asked Questions

Will material still be available after a course ends?

While access to the software will end when the course closes, some of the material within the course (slides, papers, and tutorials) are available for download so that you can refer back to it after the course. Other materials, such as videos and quizzes that you complete during the course session, will only be available within the course platform but still accessible after the course closes. Access to the software platforms will only be available for the duration of the course.

Do I need access to the software to be able to do the course? Do I have to purchase the software separately?

For the duration of the course, you will have access to a web-based version of Maestro as well as LiveDesign. You do not have to separately purchase access to these things. While access to the software will end when the course closes, some of the material within the course (slides, papers, and tutorials) are available for download so that you can refer back to it after the course. Other materials, such as videos, quizzes, and access to the software, will only be available for the duration of the course. Please note that Schrödinger software is only to be used for course-related purposes.

Do I need to know how to use Maestro/LiveDesign to be able to take this course?

No. The modules within the course will familiarize you with both interfaces and teach you how to perform tasks and execute workflows within them.

Does this course teach you how to use the software or about design principles?

Both. As this has been designed with a person who is new to molecular modeling and drug discovery in mind, the course begins with an introduction to the drug discovery pipeline and how molecular modeling fits into it. The initial modules will teach the participant how to use the software interface and perform calculations. The middle modules will look at an example system for drug discovery highlighting important decisions to make during various stages of drug design research. The final module will be a case study where participants will apply all the concepts they have learned to design and assess new compounds for a drug target.

How long do courses run? How long do I have to do the course? Do I have to complete the course by a certain time?

Schrödinger’s online course is completely asynchronous, meaning you can work at your own pace and whenever suits your schedule during a course session. Course sessions are 5 weeks in length, with all course content being available during that time. In order to be considered for a certificate and LinkedIn badge, you must complete all required elements of the course (quizzes, assignments, and the final case study) while the course is in session.


Jennifer Chambers, Ph.D.
Jennifer Chambers, Ph.D.

Schrodinger LLC

Wade Miller, Ph.D.
Wade Miller, Ph.D.

Schrodinger LLC