C2S: Condition-to-Simplex Protein Design with Response-Aware Sequence Selection

Protein design seeks sequences that realize desired behaviors, yet structure-conditioned methods largely optimize compatibility with prescribed conformations rather than behavior under a specified context. We introduce Condition-to-Simplex (C2S), which recasts condition-specific design as control over a simplex of structural states. C2S translates a functional specification into continuous state preferences and introduces $\pi$-FiLM to act on state contrasts, steering sequence probabilities according to the desired regime rather than a fixed conformation. A response model then resolves the remaining choice in functional space, selecting candidates by their predicted behavior under the specified context. Across structural-control and measured-response tasks, C2S improves both request following and functional target matching. This formulation provides a path from designing for structural states to designing for context-dependent protein behavior.Our code is available at https://anonymous.4open.science/r/papercode.