通过非平衡方法计算蛋白质自由能，高效定位柔性区域。
Conditioned free-energy density of proteins using unbalanced solutions to constraint satisfaction problems
- 将蛋白质自由能计算转化为非平衡2→1范数问题
- 在泛化结构上发现泛化区域，保持二级结构不变
- 适合研究蛋白质构象动态与功能相关柔性
我们证明，计算条件性非均匀Curie--Weiss自旋哈密顿量的对数划分函数（自由能）可归约为一个非平衡的2→1范数计算问题，并设计了一种多项式时间的SDP算法，同时给出了实现非平衡程度的下界证明。该方法应用于蛋白质泛素（Ubiquitin），从已知晶体结构出发，在自由能景观中探索替代主链构象，识别出保持天然二级结构的柔性区域。
原文摘要 · Abstract (English)
We show that computing the log-partition function (free-energy) of conditioned inhomogeneous Curie--Weiss spin Hamiltonians reduces to an unbalanced $2 \to 1$ norm computation, and design a polynomial-time SDP algorithm for this problem with a lower bound proof for the amount of unbalance achieved. Applied to the protein Ubiquitin, the framework starts from a known crystal structure, explores alternative backbone conformations across the free-energy landscape, and identifies flexible regions of the protein while preserving its native secondary structure.
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