Cellmer Troy, Fawzi Nicolas L
Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
Methods Mol Biol. 2012;899:453-70. doi: 10.1007/978-1-61779-921-1_27.
Protein aggregation is believed to be responsible for a number of human diseases and limits the yields of pharmaceutical proteins during production. Computer simulations can be used to develop novel experimentally testable hypotheses pertaining to aggregation. While all-atom simulations with explicit solvent are too computationally intensive to address the multitude of relevant time scales, coarse-grained models make it possible to observe the transition of monomers to an equilibrium containing aggregates. Here, we provide the reader with background information and a list of steps for setting up, performing, and analyzing computer simulations of aggregating coarse-grained (CG) proteins.
蛋白质聚集被认为是多种人类疾病的病因，并且在生产过程中限制了药用蛋白质的产量。计算机模拟可用于提出与聚集相关的新的可实验验证的假设。虽然具有显式溶剂的全原子模拟计算量太大，无法处理众多相关的时间尺度，但粗粒度模型使观察单体向包含聚集体的平衡态转变成为可能。在这里，我们为读者提供背景信息以及设置、执行和分析聚集粗粒度（CG）蛋白质计算机模拟的步骤列表。
