Molecular dynamics trajectories for the prostaglandin D2 receptor 1

Molecular Dynamics Data for "Structural insights into the mechanism of activation and inhibition of the prostaglandin D2 receptor 1" (Nature Communications, 2025)

Authors: Behnaz Davoudinasab, Aleksey Raskovalov, Woojin Lee, Gye Won Han, Jordy Ho Ming Lam, Vsevolod Katritch, Vadim Cherezov

Molecular dynamics (MD) simulations were performed on the prostaglandin D2 receptor 1 (DP1) in its active, inactive, and apo states. For each system, nine independent replicas of 1.2-microsecond MD simulations were carried out. This dataset includes the production trajectories saved in .xtc format, with frames recorded every 50 steps (1 step = 2 fs). The corresponding input and topology files are also included. Periodic boundary conditions can be restored using VMD's standard pbc commands.

《前列腺素D2受体1的激活与抑制机制的结构解析》（《自然·通讯》，2025年）相关分子动力学数据集

作者：贝赫纳兹·达乌迪纳萨布、阿列克谢·拉斯科瓦洛夫、李佑镇、韩桂元、林浩明、弗谢沃洛德·卡特里奇、瓦季姆·切列佐夫

本数据集针对处于激活态、失活态与无配体（apo）态的前列腺素D2受体1（DP1）开展了分子动力学（MD）模拟。针对每个模拟体系，均开展了9组独立的1.2微秒时长的分子动力学重复模拟。本数据集包含以.xtc格式存储的生产模拟轨迹，轨迹帧每50步采集一次（1步=2飞秒），同时附带对应的输入文件与拓扑文件。可通过VMD的标准周期性边界条件（Periodic Boundary Conditions，PBC）命令恢复体系的周期性边界条件。