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

2 hours
Video:
Course Overview: free energy calculations for drug design with FEP+
Checkpoint:
Honor Code agreement
Video:
Introduction to free energy perturbation and FEP+ methods
End of Module Checkpoint

Module 2

Preparing Structures for FEP+

4 hours + Compute Time
Video:
FEP+ best practices and the importance of structure preparation
Video Tutorials:
Preparing and validating proteins

Ligand preparation and alignment
End of Module Checkpoint

Module 3

Relative Binding FEP+: Setting Up and Running a Calculation

3 hours + Compute Time
Video Tutorials:
An introduction to the FEP+ panel

Map generation and running a retrospective relative binding affinity FEP+ calculation
End of Module Checkpoint

Module 4

Analyzing and Troubleshooting FEP+ Jobs

4 hours + Compute Time
Video Tutorials:
FEP+ results analysis
Assignment:
Correlation plot generation
Tutorials:
Troubleshooting FEP+ results
End of Module Checkpoint

Module 5

Small Molecule Drug Design FEP+ Guided Case Study

2 hours + Compute Time
Tutorials:
Designing new compounds and running a prospective relative binding affinity FEP+ calculation

Merging FEP+ maps: analyzing new and previously validated compounds
Assignment:
Review and discuss case study findings
Course Completion and Certification
Hands-on application of FEP+ to small molecule drug discovery.
Videos with subtitles and downloadable transcripts help give background and context

"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

Video tutorials demonstrate how to perform FEP+ calculations and analysis
Perform hands-on FEP+ calculations and analysis on a virtual cluster, without needing your own licenses or compute resources.

"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

Learn common troubleshooting techniques and advanced settings.

Course Dates

Session Dates
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]

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? [Answer]

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? [Answer]

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? [Answer]

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.
 

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.

 

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