Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden.
LINXS - Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, SE-223 70 Lund, Sweden.
J Chem Inf Model. 2023 Jul 10;63(13):4079-4087. doi: 10.1021/acs.jcim.3c00113. Epub 2023 Jun 20.
Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here. Instead, it showed the least good agreement, indicating that one should not necessarily trust the otherwise intuitive notion of a more advanced model inherently being better in model choice.
粗粒化通常用于降低模拟的计算成本。然而，粗粒化模型也被认为具有较低的可转移性，对于原始参数化范围之外的系统准确性较低。在这里，我们对珠链模型和改进的 Martini 2 模型这两种粗粒化模型进行了基准测试，这些模型针对一组固有无序蛋白质，不同的模型具有不同程度的粗粒化。SOP-IDP 模型之前已用于该组蛋白质；因此，这些结果包含在本研究中，以比较不同粗粒化水平的模型如何进行比较。对于实验蛋白质库来说，最不粗粒化模型表现最好的这种有时天真的期望并不成立。相反，它显示出最差的一致性，这表明在模型选择中，人们不应该理所当然地认为更先进的模型本质上更好。
