Introduction to molecular modeling in drug discovery

Introduction to molecular modeling in drug discovery

Protein preparation, ligand docking, collaborative design, and other fundamentals of small molecule drug discovery with Maestro and LiveDesign

5 weeks / ~20 hours to complete
$545 for non-student users
$140 for student / post-doc
Course Timeframe
When registering for the course, you will be able to choose your preferred start and end date. Within those dates, you will have asynchronous access to the course to work on your preferred schedule


Computational molecular modeling tools have proven effective in drug discovery and are increasing in use across the pharmaceutical industry. The drug hunters of today will continue to encounter molecular modeling throughout their careers making it critical to have a foundational understanding of the relevant tools and methods.

This course is ideal for those who wish to develop professionally and expand their CV by earning certification and a badge.

  • Work hands-on with Schrodinger’s Maestro and LiveDesign on your own schedule whenever convenient for you within the course session
  • Jump start your research program by learning methods that can be directly applied to ongoing projects
  • Learn topics ranging from protein structure preparation to ligand docking
  • Perform a completely independent case study to demonstrate mastery of the course content
  • Benefit from the review and feedback of Schrödinger experts for course assignments and queries


This course comes with access to a web-based version of Schrödinger software with the necessary licenses and compute resources for the course:

  • A computer with reliable high speed internet access (8 Mbps or better)
  • A mouse and/or external monitor (recommended but not required)
  • Be familiar with the concepts of protein structure, compound potency, molecular mass, and pKa
  • A certificate signed by the Schrödinger course lead
  • A badge that can be posted to social media, such as LinkedIn
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What you will learn

Maestro interface

Use an industry-leading graphical user interface for small molecule modeling. Please note that there is no coding or scripting required to run modeling workflows in this course

Fundamentals of computational drug design

Learn how computational tools are already being used on drug discovery projects, and basic theory behind some of the most common workflows

Structure and ligand-based modeling workflows

Best practices for protein and ligand preparation, structure and ligand-based virtual screening, and multi-parameter ligand optimization

Applying workflows to projects

Apply your skills in an open-ended case study where you design novel VEGR2 inhibitors using a collaborative enterprise informatics platform


Module 1
2 Hours

Introduction to modeling and scene setting

Syllabus and honor code

Expectations surrounding academic integrity


Introducing the value of molecular modeling and case studies

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Module 2
3 Hours

Fundamental tasks in the Maestro user interface

Video Tutorial
Video tutorial

Getting started and modifying small molecules

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Module 3
4 Hours

Viewing protein-ligand interactions

Video Tutorial
Video tutorials
  • Navigating the structure hierarchy and adding surfaces
  • Ligand Interaction Diagram and sharing generated images
  • Ligand preparation with LigPrep, and Ligand Alignment
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Module 4
4 Hours

Structure-based virtual screening techniques

Video Tutorial
Video tutorials
  • Choosing a virtual screening method and structure based virtual screening with ligand docking
  • Protein structure inspection and preparation, docking grid generation, and docking analysis
  • Enumeration and analysis with the Ligand Designer
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Module 5
2 Hours

Ligand-based virtual screening techniques

Video Tutorial
Video tutorial

Ligand-based virtual screening methods


Shape-based screening of a ligand database

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Module 6
4 Hours

Workflows and exercises in Livedesign

Video Tutorial
Video toturials
  • Organize data and collaborate effectively in drug discovery
  • Workflows for collaborative drug design

Ideation for drug discovery projects, including building and analyzing data in LiveDesign

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Module 7
6 Hours

Case study on VEGFR2


Background on kinase structure and activity

  • Perform docking
  • Calculate enrichment
  • Analyze hit series
  • Analog ideation
  • Enrichment submission
  • Final compound submission
Course completion
Course completion and certification

What our alumni say

“I learned new concepts even though I have been in this field for almost 30 years. The final LiveDesign exercise was particularly enjoyable and eye-opening. I recommend this course for both beginners and experience medicinal chemists.”
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Michael WaltersResearch Associate Professor, University of Minnesota
“An eye-opening and enjoyable deep-dive into the computational tools Schrödinger has developed for streamlining drug discovery for industrial and academic researchers.”
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Croix LaconsayPostdoctoral Researcher University of Houston
“I definitely learned more about molecular modeling and feeling excited for this field to grow more. I also feel like I leveled up as a medicinal chemist with the ability to use Maestro in my back pocket.”
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Tom LuongPTC Therapeutics
“The course was elegantly organized and profoundly impacted my understanding of CADD and the techniques surrounding rational ligand-receptor design.”
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Marshall LougeeGraduate Student at the University of Pennsylvania
“This course has been an amazing experience in accelerating how I work with my data, think about analyzing it, and get the most information out of it.”
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Ivana Serrano LachapelGraduate Student at Stanford University

Frequently asked questions

How much do the online courses cost?

Pricing varies by each course and by the participant type. For students wishing to take these courses, we offer a student price of $140 for introductory courses, $290 for the Materials Science bundle, and $825 for advanced courses. For commercial participants, the course price is $545 for introductory courses and $1365 for advanced courses and bundles.

When does the course start?

The courses run on sessions, which range from 3-6 week periods during which the course and access to software are available to participants. You can find the course session and start dates on each course page.

What time are the lectures?

Once the course session begins, all lectures are asynchronous and you can view the self-paced videos, tutorials, and assignments at your convenience.

How could I pay for this course?

Interested participants can pay for the course by completing their registration and using the credit card portal for an instant sign up. Please note that a credit card is required as we do not accept debit cards. Additionally, we can provide a purchase order upon request, please email if you are interested in this option.

How can I preview the course before registering?
Are there any scholarship opportunities available for students?

Schrödinger is committed to supporting students with limited resources. Schrödinger’s mission is to improve human health and quality of life by transforming the way therapeutics and materials are discovered. Schrödinger proudly supports the next generation of scientists. We have created a scholarship program that is open to full-time students or post-docs to students who can demonstrate financial need, and have a statement of support from the academic advisor. Please complete the application form if you qualify for our scholarship program!

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, quizzes, and access to the software, 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, Bioluminate, Materials Science Maestro and/or LiveDesign (depending on the course). You do not have to separately purchase access to any software. 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.

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