Molecular Dynamics Trajectories for GPR6 Basal Activity (Volume 02)

Molecular Dynamics Data for 10.1126/scisignal.ado8741 for publication at Science Signalling Barekatain M., Johansson L.C., Lam J.H. et al Structural Insights into the High Basal Activity and Inverse Agonism of the Orphan Receptor GPR6 Implicated in Parkinson's Disease, Sci Signal. 2024 Dec 3;17(865):eado8741. doi: 10.1126/scisignal.ado8741. Epub 2024 Dec 3. Instruction The compressed folder contains the PDB format file ("Topology") and the XTC format file (Trajectories). The timestep in this strided trajectory is 0.1 ns per frame.The compression was created with, for example, `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` They can be decompressed with `cat Nolig_Respawn00a.tar.* | tar xzpvf -` Remarks Trajectories in Respawn00 are only used as an initial sampling round. Trajectories in Respawn01 are the final sampling round for building Markov state model. There are in total 4 Volumes of Respawn01 data. Currently, the union of these volumes must be downloaded before decompression. See https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest For trajectories without keyword 'fitted', the Periodic boundary condition (PBC) can be restored using VMD's standard pbc commands. For`*fitted*.xtc`, the protein has already been centered and the PBC is destroyed for the sake of visual inspection only. Please cite us if you find this data useful!本数据集为发表于《Science Signalling》期刊、DOI为10.1126/scisignal.ado8741的学术论文配套分子动力学数据。 论文作者包括Barekatain M.、Johansson L.C.、Lam J.H.等，题为《与帕金森病相关的孤儿受体GPR6的高基础活性及反向激动作用的结构洞察》，发表于*Sci Signal*. 2024 Dec 3;17(865):eado8741，DOI: 10.1126/scisignal.ado8741，2024年12月3日在线发表。 ## 使用说明 本压缩包内含PDB格式拓扑文件（Topology）与XTC格式轨迹文件（Trajectories）。该分帧轨迹的时间步长为每帧0.1纳秒。压缩包可通过如下命令生成： `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` 解压命令如下： `cat Nolig_Respawn00a.tar.* | tar xzpvf -` ## 备注 1. Respawn00目录下的轨迹仅用于初始采样轮次，Respawn01目录下的轨迹为构建马尔可夫状态模型（Markov State Model）所用的最终采样轮次数据。 2. Respawn01数据共分为4个卷集，当前需下载全部卷集后方可进行解压操作。完整数据集可访问：https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest 3. 对于文件名不含「fitted」关键字的轨迹，可通过VMD的标准周期性边界条件（Periodic Boundary Condition, PBC）命令恢复周期性边界。对于`*fitted*.xtc`文件，为便于可视化观测，蛋白质已被中心化处理，此时周期性边界条件已被移除。 若您使用本数据集开展研究，请引用本论文。