Target enablement, preparation, & validation
Enabling protein structures from x-ray crystallography, cryo-EM, ML-methods, and homology modeling for structure-based computational workflows
Details
Modules
5
Duration
Up to 20 hours over 5 weeks from selected start date
Level
Intermediate
Cost
$645 for non-student users
$240 for student / post-doc
Who should take this course?
Medicinal chemists, cheminformaticians, ML scientists, new computational chemists, and structural biologists
Overview
With the explosion of available structures from x-ray crystallography, cryo-EM and, more recently, machine learning (ML) methods, there is a growing need for tools and workflows for preparing, refining and validating structures for structure-based computational workflows.
Schrödinger’s online course, Target Enablement, Preparation, and Validation will provide expert guidance and best practices to equip you to enable projects for prospective structure-based computational modeling workflows such as virtual screening, molecular dynamics simulations, and free energy perturbation calculations.
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 refining AlphaFold structures to cryptic pocket identification
- 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 and structural biology
- 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 to add to your CV or resume
- A badge that can be posted to social media, such as LinkedIn
What you will learn
X-ray and cryo-EM structures
Learn best practices for preparing and refining experimental structures of varying quality
ML-predicted structures and homology modeling
Learn best practices for working with and refining ML-predicted structures (such as from AlphaFold) and homology models
Binding site identification
Learn how to evaluate the drugability of small molecule binding site, as well as search for and characterize potential cryptic pockets
Prospective enablement of a target
Apply your skills by independently enabling a target through thorough inspection of available structures, analysis, and refinement
Modules
Module 1
2 Hours
Target enablement methods and the value of structural validation
Video
Course overview
Syllabus and honor code
Expectations surrounding academic integrity
Videos
- The importance of structure validation in computational experiments for drug discovery
- Comparing common target enablement methods
End of module checkpoint
Module 2
5 Hours
Starting point: X-ray crystal and cryogenic electron microscopy structures
Video
Structure availability and experimental considerations
Tutorials:
- Structure quality metrics
- Inspection workflows
- Protein preparation
- Basic refinement
End of module checkpoint
Module 3
4 Hours
Starting point: AlphaFold structures and homology models
Video
Generating, inspecting, and validating AlphaFold and homology models
Tutorials
- Obtaining and reviewing AlphaFold structures
- Homology modeling
- Model refinement methods
End of module checkpoint
Module 4
5 Hours
Next steps: advanced preparation, refinement, and validation of structures
Video
Refinement and validation methods for more challenging targets
Tutorials
- Manual protein preparation
- SiteMap
- Mixed Solvent Molecular Dynamics
- WaterMap
- FEP+ validation
End of module checkpoint
Module 5
4 Hours
Case study: prepare and validate a structure for computational drug discovery
Video
- Case study overview
- Case study findings and course closing
Tutorial
Structural inspection, preparation, and validation
Assignment
Review and discuss case study findings
Course completion and certification
Need help obtaining funding for a Schrödinger Online Course?
We proudly support the next generation of scientists and are committed to providing opportunities to those with limited resources. Learn about your funding options for our online certification courses as a student, post-doc, or industry scientist and enroll today!
Show off your newly acquired skills with a course badge and certificate
When you complete a course with us in molecular modeling and are ready to share what you learned with your colleagues and employers, you can share your certificate and badge on your LinkedIn profile.
Frequently asked questions
How much does the Target enablement, preparation, and validation 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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