Pseudopotentials for the chemical cross-links comprising the glutamic- and aspartic-acid side chains bridged with adipic- (ADH) or pimelic-acid hydrazide (PDH), and the lysine side chains bridged with glutaric (BS²G) or suberic acid (BS³) for coarse-grained cross-link-assisted simulations were determined by canonical molecular dynamics with the Amber14sb force field. The potentials depend on the distance between side-chain ends and on side-chain orientation, this preventing from making cross-link contacts across the globule in simulations. The potentials were implemented in the UNRES coarse-grained force field and their effect on the quality of models was assessed with 11 monomeric and 1 dimeric proteins, using synthetic or experimental cross-link data. Simulations with the new potentials resulted in improvement of the generated models compared to unrestrained simulations in more instances compared to those with the statistical potentials.

中文翻译：

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蛋白质结构粗粒度交联辅助建模的赝势

化学交联的赝势包括与己二酸 (ADH) 或庚二酸酰肼 (PDH) 桥接的谷氨酸和天冬氨酸侧链，以及与戊二酸 (BS ² G) 或辛二酸桥接的赖氨酸侧链 ( BS ³) 对于粗粒度的交联辅助模拟，由典型分子动力学和 Amber14sb 力场确定。电位取决于侧链末端之间的距离和侧链方向，这防止了在模拟中跨球体进行交联接触。在 UNRES 粗粒度力场中实施了电位，并使用合成或实验交联数据，用 11 种单体和 1 种二聚体蛋白评估了它们对模型质量的影响。与具有统计潜力的模拟相比，在更多实例中，具有新潜力的模拟导致生成的模型得到改进。