Free energy calculations for drug design with FEP+

Free energy calculations for drug design with FEP+

Running, analyzing, and troubleshooting relative binding FEP+ calculations for small molecule lead optimization

3 weeks / ~15 hours to complete
$1365 for non-student users
$825 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 methods can help drive forward drug discovery campaigns through prediction of binding affinities of small molecules to protein targets.  Free energy perturbation techniques, such as Schrödinger’s FEP+, can provide accurate predictions for binding affinities in drug design. However, these are advanced calculations that require expertise to deploy. Computational chemists and drug designers can benefit from hands-on training in running FEP+ to ensure best practices are used and thorough analysis can be done on the results. In this course you will get an overview of how Schrödinger’s FEP+ works, apply relative binding affinity FEP+ technology to several data sets, and perform common analysis techniques.

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 Schrödinger’s industry-leading FEP+
  • Jump start your research program by learning methods that can be directly applied to ongoing projects
  • Learn topics ranging from FEP+ map generation to pKa correction
  • Complete a case study by designing new compounds and running prospective FEP+ to demonstrate mastery of the course content
  • Benefit from review and feedback from Schrödinger Education Team experts for course assignments and course-related queries
  • Work on the course materials on your own schedule whenever convenient for you within the course session


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)
  • Working knowledge of general chemistry
  • Working knowledge of Maestro. This course will not teach you how to navigate the Schrödinger graphical user interface, Maestro. Please work through our Getting Started with Maestro resources to become familiar with using Maestro.
  • 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

Fundamentals of free energy perturbation

Gain and understanding of the history and theory behind free energy perturbation methods, as well as how they are already having impact on drug discovery programs

Preparing structures for FEP+

Best practices for preparing proteins and ligands for relative binding FEP+ jobs

Common troubleshooting techniques

Exploring using extended simulation times, pKa correction, Custom Cores, and adding protein residues to the REST region to improve FEP+ performance 

Applying FEP+ to projects

Apply your skills in a hands-on case study where you design novel spleen tyrosine kinase (Syk) inhibitors and profile them prospectively using FEP+


Module 1
2 Hours

Free energy perturbation introduction and scene setting


Course overview: free energy calculations for drug design with FEP+


Honor code agreement


Introduction to free energy perturbation and FEP+ methods

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End of module checkpoint
Module 2
4 Hours + Compute Time

Preparing structures for FEP+


FEP+ best practices and the importance of structure preparation

Video Tutorial
Video tutorials
  • Preparing and validating proteins
  • Ligand preparation and alignment
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End of module checkpoint
Module 3
3 Hours + Compute Time

Relative binding FEP+: setting up and running a calculation

Video Tutorial
Video tutorials
  • An introduction to the FEP+ panel
  • Map generation and running a retrospective relative binding affinity FEP+ calculation 
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End of module checkpoint
Module 4
4 Hours + Compute Time

Analyzing and troubleshooting FEP+ jobs

Video Tutorial
Video tutorial

FEP+ results analysis 


Correlation plot generation


Troubleshooting FEP+ results

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End of module checkpoint
Module 5
2 Hours + Compute Time

Small molecule drug design FEP+ guided case study

  • Designing new compounds and running a prospective relative binding affinity FEP+ calculation
  • Merging FEP+ maps: analyzing new and previously validated compounds

Review and discuss case study findings

Course completion
Course completion and certification

What our alumni say

“I was pleasantly surprised by the strong focus on structure quality assessment at the start of the course. This is an aspect that’s…overlooked in practice, in the rush to get projects off the ground, but one I feel is incredibly important.”
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Ivan SergeyevPricipal Scientist, Computational Chemistry, ROME Therapeutics
“I would highly recommend the Schrödinger online courses to anyone who wishes to learn more about applications of computational chemistry to structure-based drug design.”
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Postgraduate computational chemist
“Clear explanations […] made difficult tasks very easy to complete. The knowledge I gained helps me design experiments of my current projects and understand papers related to them much faster than before.”
Testimonial Icon
Anna DudekPostdoctoral Research, Chang Gung Medical Foundation

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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