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!对应《Science Signalling》期刊论文10.1126/scisignal.ado8741的分子动力学数据集 Barekatain M.、Johansson L.C.、Lam J.H. 等，《靶向帕金森病的孤儿受体GPR6的高基础活性与反向激动作用的结构解析》，发表于《Science Signalling》，2024年12月3日；17(865):eado8741。DOI: 10.1126/scisignal.ado8741，2024年12月3日在线发表。 使用说明 本压缩包包含PDB格式拓扑文件（"Topology"）与XTC格式轨迹文件（"Trajectories"）。该分帧轨迹的每帧对应时间步长为0.1纳秒。本压缩包可通过如下命令生成（示例）： `tar czpvf - ./Nolig_Respawn00/ | split -d -b 5000M - Nolig_Respawn00a.tar.` 可通过以下命令解压： `cat Nolig_Respawn00a.tar.* | tar xzpvf -` 备注 Respawn00组轨迹仅用于初始采样轮次，Respawn01组轨迹为构建马尔可夫状态模型（Markov State Model, MSM）的最终采样轮次。 Respawn01数据集共分为4个卷册，当前需下载所有卷册后方可进行解压操作，详情请访问：https://zenodo.org/communities/mdtrajectorygpr6/records?q=&l=list&p=1&s=10&sort=newest。 对于文件名不含"fitted"关键词的轨迹文件，可通过VMD标准PBC命令恢复周期性边界条件（Periodic Boundary Condition, PBC）；对于`*fitted*.xtc`文件，蛋白已完成居中对齐，仅为便于可视化观测而移除了周期性边界条件。 若您使用本数据集，请引用本文献！