ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning

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arXiv:2605.21600v3 Announce Type: replace Abstract: Computational antibody CDR design methods condition on antigen structure to generate binding loops. Yet, the existing architectures conflate two fundamentally distinct sub-problems: identifying which CDR positions will contact the antigen, and selecting amino acids at those positions. This forces models to learn contact reasoning implicitly through uniform message passing, diluting antigen signal across all positions equally. We introduce ConTact, a contact-then-act architecture that explicitly decomposes CDR design into three cascaded stages: learning surface complementarity fingerprints, predicting CDR-antigen contacts, and injecting contact-gated antigen features into the prediction head. A distance-biased cross-attention module encodes geometric priors favoring spatial neighbors, a contact-weighted cross-entropy loss concentrates gradient signal on binding-critical positions, and a standoff-aware contact-recovery loss places the designed loop against its native epitope. On the ChiMERa-Bench dataset, ConTact surpasses the baselines on the binding interface and structural metrics (backbone RMSD, fraction of native contacts, interface RMSD, DockQ, and epitope F1) on all three splits, improving native-contact recovery by 11 to 16%, while matching the best sequence recovery. The source code is available at: https://github.com/mansoor181/ConTact.git

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