Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam.
Methods Mol Biol. 2022;2340:51-78. doi: 10.1007/978-1-0716-1546-1_4.
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
多年来，全世界许多研究小组一直在研究蛋白质聚集，因为它可能是许多没有有效治疗方法的神经退行性疾病的原因。获得相关原纤维和毒性寡聚物的结构，以及描述控制自组织过程的途径和主要因素至关重要，但也非常困难。为了解决这个问题，实验和计算方法通常结合使用，以充分利用每种方法。计算方法的有效性在很大程度上取决于合理分子模型的构建。在这里，我们讨论了为折叠和固有无序蛋白质或两者而开发的四个最流行的全原子力场 AMBER、CHARMM、GROMOS 和 OPLS 的不同版本。还总结了主要用于研究聚集动力学的连续和离散粗粒模型。
