Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is data- and compute-hungry. With limited supervision, LLMs can produce coherent plans in text yet fail to reliably realize them as sequences. This plan–execute gap motivates ProtoCycle, an agentic framework for protein design that uses LLMs primarily to drive a multi-round, feedback-driven decision cycle. ProtoCycle couples an LLM planner with a lightweight tool environment designed to emulate the iterative workflow of human protein engineers and uses LLM-driven reflection on tool feedback to revise plans. Trained with supervised trajectories and online reinforcement learning, ProtoCycle achieves strong language alignment while maintaining competitive foldability, and ablations show that reflection substantially improves sequence quality.

We present T⋆, a simple TraceRL-based curriculum for progressive block-size scaling in masked diffusion language models (MDMs).Starting from an AR-initialized small-block MDM, T⋆ gradually increases the block size while re-optimizing the denoising policy at each stage, enabling higher-parallelism decoding with limited degradation on math reasoning benchmarks. Across two SDAR scales and three benchmarks, T⋆ consistently outperforms direct large-block TraceRL and is substantially more stable during training. Our schedule analysis suggests that the learned policy does not simply revert to a strictly left-to-right order; instead, it retains block-size-specific non-monotone updates while improving accuracy.