High-throughput virtual screening for hit finding & evaluation

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
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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

Checkpoint
Syllabus and honor code

Expectations surrounding academic integrity

Video
Videos

Introduction to high-throughput screening and this online course

End checkpoint
End of module checkpoint
Module 2
4 Hours

Virtual screening concepts and theory

Video
Video

Structure-based, ligand-based, and active learning approaches

End checkpoint
End of module checkpoint
Module 3
10 Hours + Compute Time

Target preparation and validation

Video
Video

Target validation workflow overview

Video Tutorial
Video tutorials
  • Protein structure inspection and preparation
  • Structure validation with SiteMap, Mixed Solvent Molecular Dynamics, and WaterMap
Assignment
Assignment

Preparing and validating a target

End checkpoint
End of module checkpoint
Module 4
8 Hours + Compute Time

Library preparation and pre-screening tasks

Tutorial
Tutorials
  • Library profiling and filtering
  • Preparation of cognate ligands
  • Large-ligand library preparation
  • GPU Shape Screen preparation
Video Tutorial
Video tutorial

LigPrep and docking grid generation

End checkpoint
End of module checkpoint
Module 5
10 Hours + Compute Time

Virtual screening validation and execution

Tutorial
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
Assignment

Docking validation results and conclusions

End checkpoint
End of module checkpoint
Module 6
6 Hours + Compute Time

Post-screening analysis

Tutorial
Tutorials
  • DISE-like selection
  • Clustering and rescoring
  • Consensus scoring
End checkpoint
End of module checkpoint
Module 7
4 Hours

Hit analysis next steps

Video
Videos
  • Methods for further evaluating and enriching hits
  • FEP concepts
End checkpoint
End of module checkpoint
Module 8
10 Hours + Compute Time

AmpC case study

Tutorial
Tutorials
  • AmpC Virtual screen analysis
  • Absolute binding FEP+ evaluation of chosen AmpC hits
Checkpoint
Case study checkpoint

Check your understanding before moving on

Assignment
Assignment

Absolute binding FEP+ findings  and observations

Course completion
Course completion and certification

What our alumni say

“The course was useful because I learnt extra concepts not covered in the introductory course such as SiteMap, WaterMap, profiling and filtering ligands…, as well the criteria for identification of Hits from large libraries.”
Testimonial Icon
Freebown RwereInstructor at Stanford University School of Medicine
“Taking the HTVS course was a great experience…My confidence also increased after completing the training. Not only did I learn a lot, but I also applied it to my dissertation.”
Testimonial Icon
Santosh BasnetGraduate Student at Tribhuvan University

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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