DNA G-quadruplex structures obtained through MD-based folding procedure

The dataset contains structures of DNA G-quadruplexes (G4s), obtained through steered molecular dynamics simulations, for 128 oligonucleotides capable of forming 3- and 2-tetrad G4s. The general sequence of the oligonucleotides is GxTiGxTjGxTkGx, where x = 3 or 2 for 3- and 2-tetrad G4s, respectively, while i, j, and k vary independently from 1 to 4, representing the length of loop regions. Each sequence was folded into 26 G4 topologies, and for each topology, all possible tetrad polarity patterns were considered (8 or 4 such patterns for 3- and 2-tetrad G4s, respectively). Lists of all obtained structures, with specifications of whether the given structures are properly folded, can be found in the files ‘List_of_three-tetrad_structures.csv’ and ‘List_of_two-tetrad_structures.csv’ for 3- and 2-tetrad G4s, respectively. Additionally, pictures showing all obtained structures and movies visualizing the folding simulation for exemplary G4s are attached.

本数据集收录了通过拉伸分子动力学模拟（steered molecular dynamics simulations）获得的DNA G-四链体（DNA G-quadruplexes, G4s）结构，涉及128条可形成含3个G四联体与2个G四联体的G4的寡核苷酸（oligonucleotides）。该类寡核苷酸的通用序列为GxTiGxTjGxTkGx，其中x分别对应含3个G四联体与2个G四联体的G4的取值3和2；i、j、k独立取值为1至4，用以表征环区（loop regions）的长度。每条序列均被折叠为26种G4拓扑结构（topology），针对每种拓扑结构，均考量了所有可能的G四联体极性模式（tetrad polarity patterns）：含3个G四联体的G4对应8种模式，含2个G四联体的G4对应4种模式。所有已获得结构的列表及对应结构是否正确折叠的说明信息，可分别从对应含3个G四联体的G4与含2个G四联体的G4的文件‘List_of_three-tetrad_structures.csv’与‘List_of_two-tetrad_structures.csv’中获取。此外，本数据集还附带了所有已获得结构的可视化图片，以及典型G4折叠模拟过程的动态演示视频。