Authors
Abanades, B., Roncoli, A., Bhagawati, M., Kessel, P., Imhof-Jung, S., Doerr, D., Schilz, J., Vasilaki, S., Seeger, F., Bonvin, A. M. J. J., Bonneau, R., Gligorijevic, V., Vangone, A.
Abstract
De novo antibody design promises to transform therapeutic antibody and nanobody discovery. Yet, success remains inconsistent across targets, with generative models often yielding no experimentally validated binders. Here we introduce MIMOSA (MIMic-Oriented Structural Antibody generation), a model-agnostic, inference-time framework that constrains diffusion-based antibody design pipelines to reproduce the interaction geometry and chemistry of a target's known cognate binder interface. Rather than searching for a productive interface from scratch, MIMOSA constrains generation around residue identities and geometries already known to support binding, while allowing the generative model to complete the surrounding antibody interface. We test MIMOSA on different interface topologies: contiguous motifs that fit within a single CDR loop and spatially dispersed hotspots distributed across the paratope. Applied without retraining to two architecturally distinct generators (RFAntibody and BoltzGen), this framework delivers experimentally validated binders-achieving sub-micromolar to single-digit nanomolar affinities-at 20-26% hit rates on three targets on which unconstrained methods produce zero or near-zero binders: KEAP1, uPA, and IL-8. By turning any target with a structurally characterised cognate binder into an accessible de novo design problem, this framework broadens the practical reach of generative antibody design to targets where unconstrained approaches currently fail.
Preprint server:
bioRxiv
The authors list and abstract were imported from bioRxiv on 30 Sep 2026.
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