CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design

arXiv:2603.13431v1 Announce Type: cross
Abstract: Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These methods are evaluated on different SAbDab snapshots, non-overlapping test sets, and incompatible metrics, and the literature fragments the design problem into numerous sub-tasks with no common definition. We introduce textscChimera-Bench (textbfCDR textbfModeling with textbfEpitope-guided textbfRedesign), a unified benchmark built around a single canonical task: emphepitope-conditioned CDR sequence-structure co-design. textscChimera-Bench provides (1) a curated, deduplicated dataset of textbf2,922 antibody-antigen complexes with epitope and paratope annotations; (2) three biologically motivated splits testing generalization to unseen epitopes, unseen antigen folds, and prospective temporal targets; and (3) a comprehensive evaluation protocol with five metric groups including novel epitope-specificity measures. We benchmark representative methods spanning different generative paradigms and report results across all splits. textscChimera-Bench is the largest dataset of its kind for the antibody design problem, allowing the community to develop and test novel methods and evaluate their generalizability. The source code and data are available at: https://github.com/mansoor181/chimera-bench.git