Qian Jun-Lin, Sun Li-Zhen
Department of Applied Physics, Zhejiang University of Technology, China.
Data Brief. 2022 May 15;42:108284. doi: 10.1016/j.dib.2022.108284. eCollection 2022 Jun.
The utility of the coarse-grained (CG) single-stranded DNA (ssDNA) model can drastically reduce the compute time for simulating the ssDNA dynamics. The model-matched CG potentials and the inherent potential constants can be derived by coarse-graining the experimentally measured ssDNA structures. A useful and widespread treatment of the CG model is to use three different pseudo-atoms P, S, and B to represent the atomic groups of phosphate, sugar, and base, respectively, in each nucleotide of the ssDNA structures. The three pseudo-atoms generate nine types of the structural parameters to characterize the unstructured ssDNA conformations, including three (virtual) bond lengths (P-S, S-B, and S-P) between two neighbouring beads, four bond angles (P-S-P, S-P-S, P-S-B, and B-S-P) between three adjacent bonds, and two dihedral angles (P-S-P-S and S-P-S-P) between three successive bonds. This paper mainly presents the data of normalized probability distributions of the bond lengths, bond angles, and dihedral angles for the CG ssDNAs.
粗粒化（CG）单链DNA（ssDNA）模型的实用性可以大幅减少模拟ssDNA动力学的计算时间。通过对实验测量的ssDNA结构进行粗粒化，可以推导出与模型匹配的CG势和固有势常数。对CG模型一种常用且广泛的处理方法是，在ssDNA结构的每个核苷酸中，分别使用三种不同的伪原子P、S和B来代表磷酸基团、糖基团和碱基的原子基团。这三种伪原子产生九种类型的结构参数来表征无规ssDNA构象，包括相邻两个珠子之间的三种（虚拟）键长（P-S、S-B和S-P）、三个相邻键之间的四个键角（P-S-P、S-P-S、P-S-B和B-S-P）以及三个连续键之间的两个二面角（P-S-P-S和S-P-S-P）。本文主要给出了CG ssDNA的键长、键角和二面角的归一化概率分布数据。
