Designed via bagel: https://github.com/softnanolab/bagel BAGEL formalizes protein design as the sampling of an energy function, either to optimize (find a global optimum) or to explore a basin of interest (generate diverse candidates). This energy function is composed of user-defined terms capturing geometric constraints, sequence embedding similarities, or structural confidence metrics. BAGEL also natively supports multi-state optimization and advanced Monte Carlo techniques, providing researchers with a flexible alternative to fixed-backbone and inverse-folding paradigms common in current design workflows.