Four modules, one pipeline
The Genolux Antibody Design Platform
Interface prediction, CDR scoring, developability assessment, candidate ranking — four modules running in sequence from FASTA input to a Pareto-optimal shortlist.
Module 01 — Interface Prediction
CDR–Antigen Contact Mapping
Submit an antibody Fv sequence and a target antigen (FASTA or PDB). Genolux runs AlphaFold2 variable-domain prediction on the antibody, then docks the predicted Fv against the antigen using RosettaDock. The result: per-residue contact maps identifying which CDR positions contribute to binding, including buried surface area, hydrogen bond geometry, and van der Waals contact energy at the paratope–epitope interface.
Module 02 — CDR Optimization
Affinity Scoring and Variant Ranking
Enumerate CDR loop sequence variants — single-point mutations, double mutants, or combinatorial CDR3 libraries up to 500 sequences per run. Each variant is scored for predicted binding affinity (ΔΔG) using a Rosetta REF2015 energy function trained on SAbDab structural data and SKEMPI2 binding affinity measurements (30,000+ experimentally measured interaction energies). Output: ranked variant list with per-variant Kd prediction, confidence interval, and residue-level energy contribution.
Module 03 — Developability Assessment
Seven Physicochemical Flags
A candidate that binds well in silico can still fail in the clinic if it aggregates, has poor viscosity at high concentration, or misfolds during CHO expression. Genolux runs every candidate through a 7-flag developability screen covering the physicochemical properties that correlate with late-stage attrition. Each flag produces a binary pass/warn and a continuous score you can filter on.
Module 04 — Manufacturability Ranking
Pareto-Optimal Candidate Shortlist
Affinity and developability are competing objectives — optimizing one often degrades the other. Genolux computes the Pareto front across binding affinity (ΔΔG), developability composite score, and predicted CHO expression yield. The output is a Pareto-optimal shortlist of candidates that represent the true trade-off frontier: sequences that are optimal in a practical sense, not just highest-binding. Delivered as ranked CSV, annotated PDB files, and JSON API response.
Inputs & Outputs
Accepted input formats and output deliverables
Accepted inputs
- Antibody sequence in FASTA format (Fv or full-length)
- Antigen sequence (FASTA) or 3D structure (PDB)
- Homology model (.pdb) for antigen when crystal structure unavailable
- Batch upload: up to 500 CDR variant sequences per run
- Pre-computed complex structure (.pdb) for scoring-only mode
Output deliverables
- Ranked variant CSV with ΔΔG, 7-flag scores, confidence intervals
- Annotated PDB files for top 10 Pareto-optimal candidates
- JSON API response (async, poll by job ID)
- Per-residue energy decomposition report (PDF)
- Interactive interface map visualization (embedded SVG)
Accuracy benchmarks
Validated against SAbDab holdout set
Performance evaluated on 418 antibody-antigen complexes held out from training. We report what the numbers actually are, including where accuracy degrades. Full methodology and evaluation code in Publications →
< 0.4
Kd prediction MAE
Mean absolute error in ΔΔG (kcal/mol) on SAbDab-2024 holdout set. Measured against SPR-confirmed affinities.
1.4 Å
CDR H3 loop RMSD
Median backbone RMSD for CDR H3 loops ≤ 12 residues. Accuracy drops for loops > 14 residues (see limitations).
86%
Developability flag precision
Precision of high-risk flag classification across 7 flags vs experimentally confirmed biophysical failure modes in test set.
Run your first antibody through the platform.
Early access is open. Submit a sequence and target antigen — results in under 10 minutes.