High-Throughput Virtual Screening for Hit Finding and Evaluation

A Schrödinger Online Course

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 will offer hands-on work with Schrödinger's Small Molecule Drug Discovery software and advanced techniques, such as Active Learning Glide and Absolute Binding Free Energy Perturbation.  Learn to apply workflows taught in this course to your research.

Whether you are looking for professional development, expanded skills for your CV, or a consistent way to onboard new employees, this course will provide practical applications of computational modeling relevant to a wide range of research topics. At the end of the course, you will have a chance to apply the concepts you've learned to a virtual screening case study to evaluate 2 million small molecule ligands against a drug target.

The course includes access to the relevant Schrödinger software for the duration of the course.


Session Dates Registration and Payment Deadline
February 7th, 2023 - March 21st, 2023January 31st, 2023
April 4th, 2023 - May 16th, 2023March 28th, 2023
June 6th, 2023 - July 18th, 2023May 30th, 2023



The course fee is $1300 for non-student participants and $785 for student participants. Groups of 5 or more get a $50 discount per person.


Course Outline:

This six-week course contains eight modules. The course is entirely self-paced and takes approximately 60 hours to complete. Please be aware that your time to complete the course may vary, particularly if you have less familiarity with small molecule drug discovery and medicinal chemistry.

Schrödinger online courses do not require any books or access to journals; additional references are included for those with journal access. Access to a computer with a high-speed internet connection (8 Mbps or better) and working knowledge of Maestro are required to complete the course. We recommend using a 3-button mouse with a scroll wheel during the course, if possible.

Module 1 - Introduction

  • Video: Course Overview
  • Video: High Throughput Hit Discovery
  • Video: The Benefits of Screening Ultra-Large Ligand Libraries
  • Read: Bibliography
  • End of Module Exercises


Module 2 - Virtual Screening Concepts and Theory

  • Video: Structure-Based Virtual Screening
  • Video: Active Learning in Virtual Screening
  • Video: Ligand-Based Virtual Screening
  • Read: Bibliography
  • End of Module Exercises


Module 3 - Target Validation and Preparation

  • Videos: Target Preparation for Structure-Based Virtual Screening
  • Videos: Target Validation for Structure-Based Virtual Screening
  • Assignment: Prepare and Validate Structures for Virtual Screening
  • Read: Bibliography
  • End of Module Exercises


Module 4 - Library Preparation and Pre-Screening Tasks

  • Read: Background and Bibliography
  • Tutorial Task: Library Profiling and Filtering
  • Video: Library Preparation with LigPrep
  • Video: Structure-Based Pre-Screening Tasks
  • Tutorial Task: Ligand-Based Pre-Screening Tasks
  • End of Module Exercises


Module 5 - Virtual Screen Validation and Execution

  • Tutorial Task: Setting Up a Docking Validation Study
  • Assignment: Interpret Validation Study Results
  • Tutorial Task: Screening 2 Million Compounds with Active Learning Glide
  • Tutorial Task: Screening 2 Million Compounds with GPU Shape
  • Read: Bibliography
  • End of Module Exercises


Module 6 - Post Screening Analysis

  • Tutorial Tasks: Filtering and DiSE Selection
  • Tutorial Tasks: Fingerprint Analysis and Clustering
  • Tutorial Task: Comparison of Scoring Functions
  • Read: Bibliography
  • End of Module Exercises


Module 7 - Next Steps

  • Video: Methods for Further Evaluating and Enriching Hits
  • Read: Additional FEP+ Concepts
  • Read: Bibliography
  • End of Module Exercises


Module 8 - Final Project

  • Tutorial Task: AmpC Case Study Instructions
  • Assessment Quiz: Case Study Understanding
  • Tutorial Task: Force Field Builder and Absolute Binding FEP+
  • Assignment: Report Absolute Binding FEP+ results and justify compound selection
  • Read: Case Study and Course Summary


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.

If you have any questions about the course, please email online-learning@schrodinger.com.



Welcome to the Schrödinger Training Center

Your web account gives you access to the complete library of Schrödinger training materials including videos, webinars, and tutorials. Your online course is just the beginning of your learning journey!

Learn more

Learn Wherever You Are

As companies and schools around the world close their locations and move to off-site working, the need and desire for remote learning options is paramount. Dr. Jenny Chambers discusses the challenges and opportunities that brought to Schrödinger.

Read the Blog

Back To Top