混合量子力学/分子力学 (QM/MM) 模拟：基于结构的药物设计和发现工具。,Mini-Reviews in Medicinal Chemistry

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混合量子力学/分子力学 (QM/MM) 模拟：基于结构的药物设计和发现工具。
Mini-Reviews in Medicinal Chemistry ( IF 3.3 ) Pub Date : 2022-01-01 , DOI: 10.2174/1389557521666211007115250
Prajakta U Kulkarni ₁ , Harshil Shah ₂ , Vivek K Vyas ₃

Affiliation

量子力学 (QM) 是基于物理学的理论，它在原子和亚原子水平上解释自然界的物理特性。分子力学 (MM) 通过使用经典力学构建分子系统。因此，当结合起来时，混合量子力学和分子力学 (QM/MM) 可以作为基于计算机的方法，用于计算分子结构的结构和性质数据。混合 QM/MM 结合了 QM 与准确性和 MM 与速度的优势。QM/MM 模拟还可用于研究溶液中以及蛋白质中的化学过程，并且在基于结构的药物设计 (SBDD) 和发现方面具有很大的应用范围。混合 QM/MM 也可以应用于 HTS 以导出 QSAR 模型。由于许多蛋白质晶体结构的可用性，它在计算化学中发挥着重要作用，尤其是在基于结构和片段的药物设计中。融合 QM/MM 模拟已被开发为探索凝聚相化学反应的广泛方法。在 QM/MM 模拟中，量子化学理论用于处理发生化学反应的空间；但是，其余部分是通过分子力学力场 (MMFF) 定义的。在这篇综述中，我们广泛回顾了最近有关使用和应用混合 QM/MM 模拟的配体和基于结构的计算方法来设计和发现治疗剂的文献。量子化学理论用于处理发生化学反应的空间；但是，其余部分是通过分子力学力场 (MMFF) 定义的。在这篇综述中，我们广泛回顾了最近有关使用和应用混合 QM/MM 模拟的配体和基于结构的计算方法来设计和发现治疗剂的文献。量子化学理论用于处理发生化学反应的空间；但是，其余部分是通过分子力学力场 (MMFF) 定义的。在这篇综述中，我们广泛回顾了最近有关使用和应用混合 QM/MM 模拟的配体和基于结构的计算方法来设计和发现治疗剂的文献。

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Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery.

Quantum Mechanics (QM) is the physics-based theory that explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, when combined, hybrid quantum mechanics and molecular mechanics (QM/MM) can act as computer-based methods that can be used to calculate the structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical processes in solutions, as well as in the proteins, and has a great scope in structure-based drug design (SBDD) and discovery. Hybrid QM/MM can also be applied to HTS to derive QSAR models. Due to the availability of many protein crystal structures, it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however, the rest is defined through the molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

更新日期：2021-10-07

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