Introduction to computational antibody engineering

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
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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

Video
Videos
  • Course overview
  • Introduction to computational antibody engineering
  • Introduction to workflows with Schrödinger tools
Assignment
Assignment

Development of therapeutic antibodies for the treatment of disease

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End of module checkpoint
Module 2
3 Hours

Basic tasks and workflows in BioLuminate

Video Tutorial
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
Assignment

Computational developability guidelines for antibody profiling

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End of module checkpoint
Module 3
4 Hours

Exploring your toolbox for structure-based and sequence-based design

Video Tutorial
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
Assignment

Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction

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End of module checkpoint
Module 4
5 Hours

Antibody modeling case studies

Assignment
Assignment

Engineering the surface properties of a human monoclonal antibody prevents self-association and rapid clearance in vivo

Video Tutorial
Video tutorials
  • Protein surface analysis – looking for aggregation hotspots
  • Antibody humanization and back mutations
  • Protein-protein docking and analysis
  • Residue scanning
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End of module checkpoint
Module 5
5 Hours

Final case study

Video
Video

Introduction to the final case study

Tutorial
Tutorials
  • Analyzing the A6-IFNGR1 interface
  • Alanine scanning
  • Homolog sequence analysis of IFNGR1
  • Residue scanning to improve affinity toward IFNGR1
Assignment
Assignment

Final assignment

Course completion
Course completion and certification

What our alumni say

“Schrödinger’s Introduction to Computational Antibody Engineering course is perfectly suited for molecular biologists seeking deeper insight into in silico antibody design and structure-guided engineering.”
Brad Schmier, PhD - CymbaX Founder and CEO
Brad Schmier, PhDCymbaX Founder and CEO
“The final case study assignment was especially fun, and I learned a lot from the instructor feedback I received.”
Heidi Hendrickson - Associate Professor of Chemistry Lafayette College
Heidi HendricksonAssociate Professor of Chemistry Lafayette College
“The text and video instructional materials are well-organized and participant-friendly…At the end of the course, I acquired skills and gained insights into leveraging computational tools to facilitate my research.”
Adebowale Alade - Graduate Research Assistant Baylor College of Medicine
Adebowale AladeGraduate Research Assistant Baylor College of Medicine
“As a trained structural biologist with minimal experience in computational chemistry, the course provided enough foundational knowledge for me to comfortably use the software and immediately apply it to my work.”
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Gail GuoResearch Scientist Broad Institute
“This course helped me a lot in strengthening my domain knowledge in genetic engineering and antibody design. It provides a lot of useful tools to run related analysis and to visualize antibody-antigen molecules.”
Testimonial Icon
Yuhang LiuSenior Data Scientist, Leveragen Inc.

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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Supporting associations

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