In this chapter the scale-consistent approach to the derivation of coarse-grained force fields developed in our laboratory is presented, in which the effective energy function originates from the potential of mean force of the system under consideration and embeds atomistically detailed interactions in the resulting energy terms through use of Kubo's cluster-cumulant expansion, appropriate selection of the major degrees of freedom to be averaged out in the derivation of analytical approximations to the energy terms, and appropriate expression of the interaction energies at the all-atom level in these degrees of freedom. Our approach enables the developers to find correct functional forms of the effective coarse-grained energy terms, without having to import them from all-atom force fields or deriving them on a heuristic basis. In particular, the energy terms derived in such a way exhibit correct dependence on coarse-grained geometry, in particular on site orientation. Moreover, analytical formulas for the multibody (correlation) terms, which appear to be crucial for coarse-grained modeling of many of the regular structures such as, e.g., protein α-helices and β-sheets, can be derived in a systematic way. Implementation of the developed theory to the UNIfied COarse-gRaiNed (UNICORN) model of biological macromolecules, which consists of the UNRES (for proteins), NARES-2P (for nucleic acids), and SUGRES-1P (for polysaccharides) components, and is being developed in our laboratory is described. Successful applications of UNICORN to the prediction of protein structure, simulating the folding and stability of proteins and nucleic acids, and solving biological problems are discussed.

本章介绍了在我们实验室中开发的尺度一致推导粗粒度力场的方法，其中有效能量函数源自所考虑系统的平均力势，并在结果中嵌入了原子详细的相互作用通过使用久保的集群累积展开的能量而言，主要的自由度的适当的选择，以在分析近似的推导的能量项被平均化，并在这些度全原子水平的相互作用能量的适当的表达自由。我们的方法使开发人员能够找到有效的粗粒度能量项的正确函数形式，而不必从所有原子力场中导入它们或以启发式方式导出它们。尤其是，以这种方式得出的能量项表现出对粗粒度几何形状的正确依赖性，尤其是对位向的依赖性。此外，多体（相关）项的分析公式对于许多规则结构（例如蛋白质）的粗粒度建模似乎至关重要α-螺旋和β-折叠可以系统地导出。将已开发的理论应用于统一的粗大生物模型（UNICORN），该模型由UNRES（用于蛋白质），NARES-2P（用于核酸）和SUGRES-1P（用于多糖）组成，并且是描述了在我们实验室中正在开发的产品。讨论了UNICORN在蛋白质结构预测，模拟蛋白质和核酸的折叠和稳定性以及解决生物学问题方面的成功应用。