Introduction to computational antibody engineering
Structure-based workflows for assessing and improving stability, affinity, and ‘humanness’ of antibody therapeutics with BioLuminate
Details
Modules
5
Duration
5 weeks / ~20 hours to complete
Level
Introductory
Cost
$545 for non-student users
$140 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
Computational molecular modeling tools have proven effective in antibody development and are increasing in use across the antibody discovery industry. The antibody engineers of today will frequently encounter molecular modeling throughout their careers making it critical to have foundational understanding of the relevant tools and methods.
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 BioLuminate
- Jump start your research program by learning methods that can be directly applied to ongoing projects
- Learn topics ranging from antibody structure prediction to developability analysis
- 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)
- Be familiar with the concepts of protein structure, compound potency, molecular mass, and pKa
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
BioLuminate interface
Learn how to use an industry-leading interface for biologics modeling. No coding or scripting required to run modeling workflows
Structure and sequence-based modeling
Antibody structure prediction, prepare antibody structures loaded from the PDB, structure reliability analysis, sequence alignment, and sequence annotation
Antibody modeling workflows
Best practices for developability analysis, humanization, computational mutagenesis, and antibody-antigen docking
Applying workflows to projects
Apply your skills in an open-ended case study where you will propose variants for an antibody targeting IFNGR1
Modules
Module 1
3 Hours
Introduction and overview
Videos
- Course overview
- Introduction to computational antibody engineering
- Introduction to workflows with Schrödinger tools
Assignment
Development of therapeutic antibodies for the treatment of disease
End of module checkpoint
Module 2
3 Hours
Basic tasks and workflows in BioLuminate
Video tutorials
- Getting started
- Importing, selecting, including, and styling structures
- Introducing workspace toggles, the structure hierarchy, and measurements
- Renaming chains and interacting with the project table
Assignment
Computational developability guidelines for antibody profiling
End of module checkpoint
Module 3
4 Hours
Exploring your toolbox for structure-based and sequence-based design
Video tutorials
- Protein preparation workflow and reliability analysis
- Antibody structure prediction and refinement
- Protein interaction analysis
- Introduction to the multiple sequence viewer/editor parts 1 and 2
Assignment
Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction
End of module checkpoint
Module 4
5 Hours
Antibody modeling case studies
Assignment
Engineering the surface properties of a human monoclonal antibody prevents self-association and rapid clearance in vivo
Video tutorials
- Protein surface analysis – looking for aggregation hotspots
- Antibody humanization and back mutations
- Protein-protein docking and analysis
- Residue scanning
End of module checkpoint
Module 5
5 Hours
Final case study
Video
Introduction to the final case study
Tutorials
- Analyzing the A6-IFNGR1 interface
- Alanine scanning
- Homolog sequence analysis of IFNGR1
- Residue scanning to improve affinity toward IFNGR1
Assignment
Final assignment
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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