Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents

We introduce ABLE, a benchmark for evaluating LLM agents' ability to use biological AI models (BAIMs), such as ProteinMPNN and AlphaFold3, in dual-use protein design workflows. ABLE assesses agent performance through a set of tasks spanning structure retrieval, sequence generation, and design validation. We evaluate 15 frontier models and find that seven refuse all tasks, while the remaining models exhibit substantial performance differences. Claude Sonnet 4 and Gemini 3 Pro achieve the highest scores across information retrieval, tool selection, and tool use. We further compare model performance on a subset of tasks against an expert human baseline. Our results suggest that current LLMs can substantially lower barriers to protein design, but remain inconsistent in planning, strategy generation, and integrating biological knowledge with tool use.

Scientific LLM agents have shown promise in literature reasoning, tool use, and experiment planning, but it remains unclear whether they can autonomously improve large, tightly coupled scientific machine-learning systems through executable code changes and computationally expensive validation. We study this question in protein folding, where progress requires coordinated architectural modifications, multi-objective evaluation, and domain-aware interpretation. We present AgentFold, a multi-agent framework that formulates folding-model development as a closed-loop search over executable code variants. Starting from ESMFold, AgentFold proposes hypotheses, implements and debugs code-level modifications, evaluates model variants, analyzes experimental outcomes, and stores both successful and failed interventions in structured memory. An MCTS-style policy allocates computational resources across high-scoring search branches. On an engineering-scale protein-folding codebase comprising more than 2,000 lines of code, AgentFold explores approximately 80 model variants using approximately 5,000 GPU-hours and 170 million LLM tokens. Under a matched computational budget, AgentFold improves the best lDDT by 7.5% over independent Codex proposals and outperforms a random-search control. Beyond model improvement, the resulting intervention traces reveal recurring empirical design patterns: stable gains tend to arise from early, soft, learnable priors and gated refinement, whereas direct geometric perturbations and geometry-conditioned feedback often destabilize training. The code and experimental resources are publicly available at https://github.com/lmqfly/AgentFold.

Real-world molecular design remains challenging for large language model (LLM)-based agents. It requires them to interpret design contexts, satisfy multiple constraints, identify infeasible specifications, and reason over multi-step tool outputs. Existing benchmarks do not capture this complexity, focusing instead on explicit and narrow constraints, only feasible problems, and single-path solutions. To address this gap, we propose MolDesignBench, a scenario-grounded benchmark that more closely reflects real-world molecular design for evaluating tool-augmented LLM agents. MolDesignBench comprises 2K generation and optimization instances that combine implicit requirements embedded in design narratives with explicit property and functional-group constraints, including infeasible cases, and require the effective use of 17 specialized chemistry tools. Experiments across diverse frontier LLMs reveal low success rates--with the best achieving only $\sim43$%--and frequent failures in implicit-constraint reasoning, infeasibility detection, and tool reasoning. The corresponding fine-grained failure-mode analysis identifies implicit constraint interpretation and infeasibility detection as the primary bottlenecks, establishing MolDesignBench as a rigorous testbed to guide future research on chemical agents. The benchmark, tool interface, and evaluation code are publicly available.