High-throughput virtual screening for hit finding & evaluation
Computational target analysis, as well as best practices for both structure-based and ligand-based virtual screening of large ligand libraries
Details
Modules
8
Duration
6 weeks / ~60 hours to complete
Level
Advanced
Cost
$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
Overview
With the substantial expansion of both virtual and physical ligand libraries, there is growing interest in using computational methods to identify hits by rapidly assessing ligands for protein targets of interest. Schrödinger’s online course, High-Throughput Virtual Screening for Hit Finding and Evaluation, will teach best practices for virtual screening of large ligand libraries.
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 virtual screening workflows
- Jump start your research program by learning methods that can be directly applied to ongoing projects
- Learn topics ranging from compound library analysis to hit ranking with Schrodinger’s absolute binding free energy perturbation (AB-FEP+) implementation
- Complete a case study and run AB-FEP+ calculations for chosen hits 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
Fundamentals of structure and ligand-based virtual screening
Methodologies behind ligand docking, pharmacophore-based screening, shape-based screening, and active learning-based workflows
Computational target analysis
Assess the quality of your target and it’s amenability to be used for structure-based drug discovery workflows
Large scale virtual screening
Set-up, run, evaluate, and post-process large scale structure-based and ligand-based virtual screens
Prospective applications of HTVS
Apply your skills by virtually screening a 2 million compound library and complete a case study to identify novel AmpC inhibitors
Modules
Module 1
4 Hours
Introduction and scene setting
Syllabus and honor code
Expectations surrounding academic integrity
Videos
Introduction to high-throughput screening and this online course
End of module checkpoint
Module 2
4 Hours
Virtual screening concepts and theory
Video
Structure-based, ligand-based, and active learning approaches
End of module checkpoint
Module 3
10 Hours + Compute Time
Target preparation and validation
Video
Target validation workflow overview
Video tutorials
- Protein structure inspection and preparation
- Structure validation with SiteMap, Mixed Solvent Molecular Dynamics, and WaterMap
Assignment
Preparing and validating a target
End of module checkpoint
Module 4
8 Hours + Compute Time
Library preparation and pre-screening tasks
Tutorials
- Library profiling and filtering
- Preparation of cognate ligands
- Large-ligand library preparation
- GPU Shape Screen preparation
Video tutorial
LigPrep and docking grid generation
End of module checkpoint
Module 5
10 Hours + Compute Time
Virtual screening validation and execution
Tutorials
- Docking validation with cognate ligands
- Docking validation enrichment study
- Structure-based virtual screen with Active Learning Glide
- Ligand-based virtual screen with GPU Shape
Assignment
Docking validation results and conclusions
End of module checkpoint
Module 6
6 Hours + Compute Time
Post-screening analysis
Tutorials
- DISE-like selection
- Clustering and rescoring
- Consensus scoring
End of module checkpoint
Module 7
4 Hours
Hit analysis next steps
Videos
- Methods for further evaluating and enriching hits
- FEP concepts
End of module checkpoint
Module 8
10 Hours + Compute Time
AmpC case study
Tutorials
- AmpC Virtual screen analysis
- Absolute binding FEP+ evaluation of chosen AmpC hits
Case study checkpoint
Check your understanding before moving on
Assignment
Absolute binding FEP+ findings and observations
Course completion and certification
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 online-learning@schrodinger.com 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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