Designing quality ligand libraries
Exploring chemical space, profiling and tailoring ligand libraries, validating docking models, and methods of enumeration for hit discovery
Details
Modules
5
Duration
5 weeks / up to 20 hours
Level
Intermediate
Cost
$645 for non-student users
$240 for student / post-doc
Course Timeframe
Self-guided over five weeks. When registering for the course you will select the start and end date. Within those dates, you will have asynchronous access to the course material and virtual workstation to work on the course when it best suits your schedule.
With the substantial expansion of both virtual and physical ligand libraries, there is growing interest in filtering and profiling these libraries to be target and project specific prior to using them for hit discovery workflows such as high-throughput virtual screening.
Schrödinger’s online course, Designing Quality Ligand Libraries will teach library design best practices, as well as how to prepare and use ligands for model validation.
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 Maestro and command line interface
- Jump start your research program by learning methods that can be directly applied to ongoing projects
- Learn topics ranging from reaction-based enumeration to library profiling
- Independently perform a case study 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:
Requirements
- 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.
Certification
- A certificate signed by the Schrödinger course lead
- A badge that can be posted to social media, such as LinkedIn
What you will learn
Fundamental concepts of real and theoretical chemical space
Profile vendor libraries to assess their composition and perform various enumeration exercises to generate in-silico enumerated libraries
The library design process
Learn strategies and considerations of filtering ligand libraries to remove clear liabilities while maintaining diversity
Enrichment calculations for model validation
Learn popular decoy generation tools as well as various alternate approaches to build appropriate decoy/unknown ligands for your research project
Prospective applications of Library Design for HTVS
Apply your skills by independently preparing a ligand library to meet target and project-specific requirements
Modules
Module 1
2 Hours
The value of quality ligand libraries for high throughput virtual screening
Syllabus and honor code
Expectations surrounding academic integrity
Videos
- Course overview
- Virtual screening overview videos and the importance of quality ligand libraries for virtual screening workflows
End of module checkpoint
Module 2
6 Hours
Generating chemical space and using commercial ligand libraries
Video
- Methods of generating chemical space
- Understanding commercial libraries and the library design process
Tutorials
- R-group and reaction-based enumeration
- Library profiling
End of module checkpoint
Module 3
4 Hours
Filtering and preparing ligand libraries
Video
- Strategies of filtering ligand libraries
- Ligand preparation for virtual screening and HTVS next steps
Tutorials
- Perform substructure and liability filtering
- Perform LigPrep and prepare for shape screening
End of module checkpoint
Module 4
4 Hours
Building ligand libraries for model validation
Video
- The purpose of ligand libraries for model validation
- Other methods of generating decoy ligand sets
Tutorial
Generate, filter, prepare, and apply a decoy ligand set for enrichment analysis
End of module checkpoint
Module 5
6 Hours
Final case study: Design a ligand library independently
Videos
- Case study overview
- Case study findings and course closing
Tutorial
Generate, filter, prepare, and assess a ligand library for a new project
Assignment
Review and discuss case study findings
Course completion and certification
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Frequently asked questions
How much does the Library Design online course cost?
Pricing varies by each course and by the participant type. For students wishing to take this, we offer a student price of $240, and $645 for non-students.
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 online-learning@schrodinger.com if you are interested in this option. If you have any questions regarding how to pay for the course, please visit our funding options page.
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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