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Products

Find the right model or tool for your drug discovery work.

AI/ML models and tools available now on TuneLab

Model

AbLab v1, v2

Predicts antibody developability across 22 endpoints, including stability, aggregation, and solubility, from sequence alone.

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Model

Antibody-Antigen Binding Affinity (ΔΔG)

TuneLab’s Antibody–Antigen Binding Affinity model predicts how a specific mutation changes binding affinity between an antibody and its antigen.

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Model

ChemLab v1, v2 Federated

Predicts ADMET and physicochemical properties to help prioritize compounds for synthesis.

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Model

Immunogenicity Model (MHC-II Peptide Presentation)

Predicts MHC class II presentation likelihood and 9-mer binding cores for antibody peptides across 12 HLA-DRB1 alleles.

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Model

in vivo PK (developed by insitro)

Predicts preclinical in vivo PK, including clearance and Vss, across multi species, developed by insitro for Lilly.

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Model

NanoLab (VHH Developability)

Predicts five biophysical developability endpoints for VHH nanobody sequences to rank leads before wet lab testing.

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Workflow

Small Molecule Computational Workflows

Configurable workflows that generate, filter, score, predict properties and rank small molecules to automate drug discovery campaigns.

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Immunogenicity Model (MHC-II Peptide Presentation)
Model

TuneLab’s Immunogenicity (MHC-II Peptide Presentation) model predicts which peptides from an antibody sequence are likely to be presented on MHC class II — the key upstream step in mounting an anti-drug antibody response. For any input sequence, it returns a presentation likelihood for each peptide across a panel of 12 common HLA-DRB1 alleles, together with the predicted 9-mer binding core.
It is trained on public data, combined with experimentally observed MAPPs peptides from Lilly proprietary therapeutic antibody data.¹⁻³ It is built for biologics engineers who need to rank candidate sequences on immunogenicity risk and pinpoint the specific residues worth re-engineering, before committing to wet lab studies.

What does the model provide?
  • Simultaneous peptide-presentation predictions across 12 HLA-DRB1 alleles, so a sequence can be assessed for broad population coverage.

  • Identification of the predicted 9-mer binding core within each presented peptide, localizing the liability to specific residues so de-immunization edits can be designed and re-scored.

Technical specifications
Modality
Antibody (peptide sequences also accepted).
Input format
Amino acid sequence — heavy and/or light chain, or individual peptides.
Output format
Returns chain, peptide sequence, HLA-DRB1 allele, predicted presentation probability, and the highest-attention binding register with its weight.
Training data type
Public MHC-II binding and eluted-ligand datasets from NetMHCIIPan, MHC Motif Atlas, and IEDB (Immune Epitope Database) combined with experimentally observed MAPPs (MHC class II associated peptide proteomics) peptides from a large Lilly panel of parent monoclonal antibodies, across 12 HLA-DRB1 alleles.
Predicted endpoint(s)
Peptide presentation (binary classification) and 9-mer binding-core identification, evaluated on a held-out test set built by clustering parent antibodies so that test sequences are distinct from those seen in training. Benchmarked head-to-head against a widely used licensed alternative on the same test set.
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FAQs
What does a high score actually mean?
It means the peptide is likely to be presented on MHC class II for that allele, which is a necessary upstream step in an anti-drug antibody response — not a prediction of clinical immunogenicity itself. Treat it as a risk flag for prioritization rather than a clinical readout.
How should I use this in a design campaign?
Use it to rank candidate sequences against one another and to locate the specific binding cores driving risk, then design substitutions in those cores and re-score. It is most reliable as a comparative tool within a campaign rather than against a fixed absolute threshold.
Why 12 alleles?
The 12 HLA-DRB1 alleles covered were selected to span common variants across major population groups, so a single run gives a reasonable view of population-level risk.
How does it compare with existing tools?
On a held-out test set of antibodies distinct from those used in training, it showed improved peptide-presentation classification performance relative to a widely used licensed alternative, with comparable performance on 9-mer binding-core identification. Because a substantial part of its training signal comes from experimentally observed MAPPs peptides from therapeutic antibodies, it is particularly well suited to antibody sequence space.
Does this replace an experimental MAPPs assay?
No. It is designed to reduce the number of candidates that need experimental MAPPs characterization and to focus engineering effort. Wet lab confirmation remains appropriate before progression decisions.
How does this relate to dendritic cell internalization?
Presentation on MHC class II is the second step in the pathway that generates anti-drug antibodies; the first is uptake and endo-lysosomal processing of the antibody by dendritic cells. Lilly measures that first step with a published FRET-based assay in which the probe fluoresces only once the antibody has been internalized and cleaved.⁴ A prediction of that assay is also available today as the DC Internalization Index endpoint within AbLab, so the two models can be read together for a fuller view of immunogenicity risk.
Reference
  • ¹(B. Reynisson et al., “NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data,” Nucleic Acids Research, vol. 48, no. W1, pp. W449–W454, 2020, doi: 10.1093/nar/gkaa379)
  • ²(D. M. Tadros, S. Eggenschwiler, J. Racle, and D. Gfeller, “The MHC Motif Atlas: a database of MHC binding specificities and ligands,” Nucleic Acids Research, vol. 51, no. D1, pp. D428–D437, 2023, doi: 10.1093/nar/gkac965)
  • ³(R. Vita et al., “The Immune Epitope Database (IEDB): 2018 update,” Nucleic Acids Research, vol. 47, no. D1, pp. D339–D343, 2019, doi: 10.1093/nar/gky1006.)
  • ⁴Wen Y, Cahya S, Zeng W, et al. Development of a FRET-Based Assay for Analysis of mAbs Internalization and Processing by Dendritic Cells in Preclinical Immunogenicity Risk Assessment. The AAPS Journal 22, 68 (2020). doi:10.1208/s12248-020-00444-1
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