Free Energy Calculations for Drug Design with FEP+
A Schrödinger Online Course
Computational methods can help drive forward drug discovery campaigns through prediction of binding affinities of small molecule 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, drug designers, and academics 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 ~15-hour long course over three weeks, 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. Beginning with structure preparation and set up, course participants will learn how to create an FEP+ map, submit calculations, and analyze results for small-molecule drug design. Next, participants will learn how to customize FEP+ calculations for their structures with using pKa correction and modifying the REST region of proteins/ligands. Finally, participants will apply what they learned to a case study to gauge their understanding of the course material.
This course comes with access to a web-based version of Schrödinger software with the necessary licenses and compute resources for the course. Participants need to have a computer with reliable, high-speed internet access (8 Mbps or better), a mouse is also recommended but not required. Participants who complete the course will receive a certificate and badge that can be posted to their social media, such as LinkedIn.
Explore Course Syllabus
Free Energy Calculation for Drug Design with FEP+: Course Structure
Module 1
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

Module 2
Preparing Structures for FEP+

FEP+ best practices and the importance of structure preparation

Preparing and validating proteins
Ligand preparation and alignment

Module 3
Relative Binding FEP+: Setting Up and Running a Calculation

An introduction to the FEP+ panel
Map generation and running a retrospective relative binding affinity FEP+ calculation

Module 4
Analyzing and Troubleshooting FEP+ Jobs

FEP+ results analysis

Correlation plot generation

Troubleshooting FEP+ results

Module 5
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



"In this ~15-hour long course over three weeks, I got a complete overview of how Schrödinger's FEP+ works, applied relative binding affinity FEP+ technology to several data sets, and performed common analysis techniques. [...] I would like to thank the Schrödinger Education team for making such an advanced-level course an easy one to follow through!"
- Suhasini Murali Iyengar, Ph.D Candidate at Northeastern University


"As a computational chemist by training, this course was helpful to me in more ways than I had imagined! I am excited to apply all the concepts I just learned to my own drug discovery projects. 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!"
- Postgraduate Computational Chemist

Course Dates
Session Dates |
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September 21st, 2023 - October 12th, 2023 |
September 28th, 2023 - October 19th, 2023 |
October 5th, 2023 - October 26th, 2023 |
October 12th, 2023 - November 2nd, 2023 |
October 19th, 2023 - November 9th, 2023 |
October 26th, 2023 - November 16th, 2023 |
November 9th, 2023 - November 30th, 2023 |
November 16th, 2023 - December 7th, 2023 |
Cost
A 15-hr online course used with evaluations or post-sales for FEP+ Models, allowing people to learn FEP+ without using their compounds via web-based Maestro. Includes a case study with a final assignment that requires grading.
- $1300 for non-student users
- $785 for student users
Course Materials
Schrödinger’s online course does not require any books nor access to specific journals (though many references are included for those who do have journal access). Access to relevant Schrödinger software is included for the duration of the course. 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.
Course Requirements
A working knowledge of general chemistry and access to a computer with a high-speed internet connection (8 Mbps or better). You can check your internet speed here.
Course Content
The Free Energy Calculations for Drug Design with FEP+ Schrödinger Online Course has been designed to equip researchers with the best practices and workflows setting up, running and analyzing relative binding affinity FEP+ calculations for small molecule drug discovery in Schrödinger. With access to Schrödinger software via cloud-based virtual workstations provisioned for the 3-week course session, participants will have the opportunity to work through approximately 15 hours of training content, including several hands-on tutorials which demonstrate the application of advanced Schrödinger tools including Force Field Builder and relative binding affinity Free Energy Perturbation (FEP+). Participants will learn common troubleshooting techniques for relative binding affinity FEP+ calculations and be able to gauge their understanding of the course content through formative checkpoint questions and case study assignment. In the final case study assignment, participants are able to design their own compounds for a pre-specified target and run a relative binding affinity FEP+ calculation, mimicking a lead optimization campaign.
FAQ
• Will material still be available after a course ends? [Answer]
• Do I need access to the software to be able to do the course? Do I have to purchase the software separately? [Answer]
• Do I need to know how to use Maestro/LiveDesign to be able to take this course? [Answer]
• Does this course teach you how to use the software or about design principles? [Answer]
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 online-learning@schrodinger.com.