Use Case — Antibody Optimization

Score CDR mutations before the expression run.

Antibody optimization campaigns burn time and budget on expression and SPR screening of variants that are predictably worse. ProtSynq ranks CDR substitutions by predicted binding ΔΔG so your expression list starts with the variants most likely to improve.

Request Access Binding ΔΔG Method
Computational workflow

The antibody optimization workflow with ProtSynq

Step 01

Complex structure in

Upload the antibody–antigen complex PDB. ProtSynq identifies the CDR loops automatically and maps the binding interface — each position's contact network, buried surface area contribution, and role in paratope geometry.

Step 02

Binding ΔΔG scan

ProtSynq scores all single-residue substitutions across CDR regions, returning a per-position binding ΔΔG heatmap. Positions that tolerate substitution without binding loss are flagged; positions critical to the binding geometry are marked as high-risk.

Step 03

Affinity + stability shortlist

Final output is a ranked list of CDR variants with predicted ΔΔG binding (affinity), predicted ΔΔG stability (Fv domain stability), and confidence bands. Select based on your Pareto tradeoff: maximum affinity gain, or balanced affinity + stability improvement.

Performance on antibody interface predictions

Evaluated against published alanine scanning datasets and deep mutational scanning studies of therapeutic antibody interfaces. Internal validation only — not published.

r = 0.71
Binding ΔΔG Pearson r
Correlation with experimentally measured KD shift for single-residue CDR substitutions on held-out test set.
~3 months
Typical time savings
Estimated reduction in optimization campaign duration when ProtSynq shortlisting replaces full CDR saturation mutagenesis library screening.
CDR1–3
H and L chain coverage
All six CDR loops (CDR-H1, -H2, -H3, CDR-L1, -L2, -L3) scored in a single run. Framework positions included on request.

Shorten your next optimization round.

Upload the antibody–antigen complex and get a ranked CDR substitution list. Research tier: ten structure jobs per month. Institutional tier: unlimited.

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