Antibody and Antigen Structural Design — Hands-on

Learn how to think about and work with antibody and antigen structures for discovery, engineering and mechanistic studies. This module walks through antibody architecture, CDR modeling, epitope and paratope mapping, complex modeling and basic stability checks so that you can generate and interpret structural designs that are ready for downstream docking, MD and developability assessments.

Antibody & Antigen Structural Design

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Session Index

Session 1 — Antibody Architecture & Antigen Basics Session 2 — Antibody Modeling, CDR Loops & Refinement Session 3 — Epitope Mapping & Antibody–Antigen Complexes Session 4 — Mini Capstone: Antibody–Antigen Design Storyboard

Session 1

Fee: Rs 8800

Antibody Architecture & Antigen Basics

Antibody structure and domain organization

heavy and light chains variable vs constant domains Fab, Fc and scFv style formats

CDRs, frameworks and paratope concepts

different CDR numbering schemes idea framework regions and scaffolds paratope surfaces and footprints

Antigen forms and epitope types overview

linear vs conformational epitopes protein vs peptide antigens surface exposure and accessibility ideas

Session 2

Fee: Rs 11800

Antibody Modeling, CDR Loops & Refinement

Template based antibody modeling ideas

germline and known scaffolds heavy and light variable regions VH VL orientation considerations

CDR loop conformations and refinement

canonical classes idea (short loops) H3 loop challenges concept local relaxation and clash removal

Basic quality checks for antibody models

geometry and Ramachandran view CDR exposure and packing developability risk motifs overview

Session 3

Fee: Rs 14800

Epitope Mapping & Antibody–Antigen Complexes

Epitope prediction and mapping ideas

surface exposure and conservation cues patch based epitope candidates using experimental hints when available

Setting up antibody–antigen docking scenarios

paratope and epitope constraints global vs local docking ideas steric feasibility and orientation checks

Interpreting complexes and interaction fingerprints

hydrogen bonds and salt bridges hydrophobic and aromatic contacts hotspot and paratope residue roles

Session 4

Fee: Rs 18800

Mini Capstone: Antibody–Antigen Design Storyboard

Define a design question for a chosen antibody–antigen pair

Theory + Practical

Build or refine complex model and summarize interactions

identify key paratope and epitope residues simple stability or contact persistence checks suggest candidate positions for tuning affinity

Deliverables: complex structure, interaction tables and design notes

PDB of complex and session notebook summary of paratope and epitope features outline for future engineering and MD work

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Antibody and Antigen Structural Design Training | CDR Modeling, Epitope Mapping & Complex Analysis

Antibody and Antigen Structural Design — Hands-on