用多智能体闭环优化量子蛋白质折叠,提升结构预测精度与成功率。
QFoldAgent: An Autonomous Quantum Optimization Multi-Agent System for Protein Structure Prediction

- 设计智能体生成序列条件惩罚,量子-经典流水线在噪声下优化哈密顿量
- 在已知结构数据上中位数RMSD从3.64降至3.20Å,未见序列有效性提升至98.7%
- 适合关注量子计算辅助结构预测的科研人员,尤其对小片段折叠研究者
混合量子-经典蛋白质结构预测高度依赖哈密顿量惩罚权重,但现有基于晶格的流程通常人工固定系数,且仅模拟极短片段。我们提出QFoldAgent,一个用于5残基四面体晶格折叠的闭环多智能体框架:设计智能体提出序列条件惩罚,基于VQE的量子-经典流水线在Qiskit Aer噪声下优化哈密顿量,反馈智能体通过能量景观诊断与MolProbity验证信号迭代优化惩罚。真实指标如RMSD不暴露给智能体,仅用于评估。我们在两个互补数据集上测试:55个来自QDockBank的已知结构片段,以及100个覆盖优化的未见序列。在QDockBank基准上,QFoldAgent将中位数RMSD从3.64 Å降至3.20 Å,最难目标改善最显著;在未见序列上,闭环使结构有效性从87.5%提升至98.7%,恢复87%初始无效案例,最强控制器在87%序列上改善第3轮能量,同时保持96%的拉马查兰有利几何。结果表明,迭代智能体控制可系统性提升5残基量子设置下的优化行为并减少失败案例。
原文摘要 · Abstract (English)
Hybrid quantum-classical protein structure prediction depends strongly on Hamiltonian penalty weights, yet existing lattice-based workflows typically fix these coefficients by hand and evaluate only very short fragments in simulation. We present QFoldAgent, a closed-loop multi-agent framework for 5-residue tetrahedral-lattice folding in which a design agent proposes sequence-conditioned penalties, a VQE-based quantum-classical pipeline optimizes the resulting Hamiltonian under Qiskit Aer noise, and a feedback agent uses energy-landscape diagnostics and MolProbity validation signals to refine penalties across cycles. Ground-truth metrics such as RMSD are never exposed to the agents and are used only for evaluation. We study the framework on two complementary datasets: 55 QDockBank-derived fragments with known structures and 100 coverage-optimized unseen sequences. On the QDockBank benchmark, QFoldAgent reduces median RMSD from 3.64 Å to 3.20 Å, with the largest gains on the hardest targets. On unseen sequences, the closed loop raises structural validity from 87.5% to 98.7%, recovers 87% of initially invalid cases, and the strongest controller improves cycle-3 energy on 87% of sequences while maintaining 96% Ramachandran-favored geometry. These results show that iterative agent control can systematically improve optimization behavior and reduce failure cases in a 5-residue quantum setting.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。