Kilian Maire

Repertoire2Structure (R2S) is a multi agent pipeline, orchestrated by Claude, that turns a raw 10x single cell TCR repertoire into QC'd predicted TCR to peptide MHC structures for its top clonotypes, with honest specificity annotation and skeptical structure QC. A researcher drops a 10x contig CSV. A team of Claude agents then runs it end to end: an intake agent frames the run (data, question, compute route), a specificity annotator matches each clonotype by TCRdist against labeled references and refuses to force a label, a structure strategist reasons about the biological question and routes each group of clonotypes to the right folding tool (Protenix by default, with TCRdock, MHC-Fine, and an AF2 presentation classifier wired in), per tool executors build the folds on Colab or a local GPU, and a skeptical QC agent calibrates every structure against a scrambled peptide control before it will call it trustworthy. Two honesty rules are enforced in the output schemas, not just narrated: specificity is annotation by similarity, never prediction; and a predicted structure never confirms specificity. What we found is an honest, convergent negative. On a preregistered repertoire benchmark, structural confidence reads peptide presentation, not TCR recognition, the same conclusion a parallel AlphaFold 3 study (McMaster et al.) reached the same month with a different engine. So R2S does not oversell a specificitrs: the reusable contribution isthe agentic question to structure system plus the guardrails a working immunologist actually needs, leakage aware annotation, pe a fold is spent, and scramblecalibrated QC that is honest about what a fold can and cannot prove.

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