Computational Antibody Affinity Maturation — Hands-on

Systematically mature antibodies in silico. Learn to quantify paratope–epitope quality, run mutational scans, design focused libraries under developability constraints, and triage candidates with docking/MD/free-energy estimates—then bundle everything into clear, defensible reports.

Computational Antibody Affinity Maturation

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Session Index

Session 1 — Interface Basics & Metrics Session 2 — In Silico Mutational Scanning Session 3 — Library Design & Multi-objective Triage Session 4 — Mini Capstone: Design → Rank → Report

Session 1

Fee: Rs 6300

Interface Basics & Metrics

Paratope–epitope anatomy, contacts, hotspots & energetics

Theory

Quantifying interfaces and spotting liabilities

buried SASA H-bonds/salt bridges hydrophobic patches

Preparing structures for design

cleanup/repair loop checks/glycans

Session 2

Fee: Rs 8400

In Silico Mutational Scanning

ΔΔG prediction & hotspot discovery (overview & practice)

Rosetta ddG FoldX DL predictors (overview)

Saturation & combinatorial scanning in CDRs

single/double mutants positional scoring synergy checks

Quick sanity: clashes, geometry & interface recovery

minimization contact maps

Session 3

Fee: Rs 11200

Library Design & Multi-objective Triage

Focused library design under developability constraints

patchiness/aggregation liabilities filters germline proximity

Docking, MD & scoring for shortlist triage (overview)

RosettaDock/HADDOCK short MD relax MM-GBSA snapshot

Ranking & uncertainty: consensus and bootstraps

score ensembles replicates

Session 4

Fee: Rs 14000

Mini Capstone: Design → Rank → Report

Propose mutations, evaluate ΔΔG, triage with docking/MD, and deliver a ranked shortlist

Theory + Practical

Provenance & reproducibility (configs, seeds, versions, logs)

YAML/JSON configs workflow scripts Quarto summary

Deliverables: figures, tables, README & manifest

PDF CSV/TSV checksums

PDF

Computational Antibody Affinity Maturation Training | Mutational Scans, Library Design & Multi-objective Triage

Computational Antibody Affinity Maturation — Hands-on