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.

Predicting the types and affinities of protein-protein interactions (PPIs) is crucial for understanding biological processes and developing novel therapeutic approaches. While encoding proteins themselves is essential, PPI networks can also provide rich prior knowledge for these predictive tasks. However, existing methods oversimplify the problem of PPI prediction in a semi-supervised manner when utilizing PPI networks, limiting their practical application. Furthermore, how to effectively use the rich prior knowledge of PPI networks for novel proteins not present in the network remains an unexplored issue. Additionally, due to inflexible architectures, most of existing methods cannot handle complexes containing an flexible number of proteins. To overcome these limitations, we introduce LLaPA (Large Language and Protein Assistant), a multimodal large language model that integrates proteins and PPI networks. LLaPA offers a more rational approach to utilizing PPI networks for PPI prediction and can fully exploit the information of PPI networks for unseen proteins. Through natural language instructions, LLaPA can accept flexible number of protein sequences and has the potential to perform various protein tasks. Experiments show that LLaPA achieves state-of-the-art performance in multi-label PPI (mPPI) type prediction and is capable of predicting the binding affinity between multiple interacting proteins based on sequence data.