Simulation Trajectories: "Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor"

Name: Simulation Trajectories: "Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor"
Creator: figshare
Published: 2020-08-27 17:01:44
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DataCite Commons2020-08-27 更新2024-07-27 收录

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* Simulations described in the following paper:Miao Y & McCammon JA (2016) Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor. Proc Natl Acad Sci U S A, 113(43):12162–12167. PMCID: PMC5087018. * Simulation lengths: system 4mqs-apo-pro-mem-wb-0.15MID 1 2 3duration(ns) 410 460 430 system 3uon-apo-c36-pro-mem-wb-0.15MID 1 2 3duration(ns) 400 400 400 system 3uon-c36-pro-mem-wb-0.15MID 1 2 3duration(ns) 405 405 400 system 4mqs-nb-arc-pro-mem-wb-0.15MID 1 2 3duration(ns) 402 405 400 system 4mqs-nb-ixo-pro-mem-wb-0.15MID 1 3 2duration(ns) 500 400 500 system 4mqs-arc-pro-mem-wb-0.15MID 1 2 3 4 5 6 7 8 9 10duration(ns) 2030 1520 1190 650 650 650 620 600 600 540 system 4mqs-ixo-pro-mem-wb-0.15MID 1 2 3 4 5 6 7 8 9 10duration(ns) 1050 1000 940 500 500 500 500 480 450 410 * List of simulation trajectores:3uon-c36-pro-mem-wb-0.15M-sim-1.nc3uon-c36-pro-mem-wb-0.15M-sim-2.nc3uon-c36-pro-mem-wb-0.15M-sim-3.nc4mqs-arc-pro-mem-wb-0.15M-sim-1.nc4mqs-arc-pro-mem-wb-0.15M-sim-2.nc4mqs-arc-pro-mem-wb-0.15M-sim-3.nc4mqs-arc-pro-mem-wb-0.15M-sim-4.nc4mqs-arc-pro-mem-wb-0.15M-sim-5.nc4mqs-arc-pro-mem-wb-0.15M-sim-6.nc4mqs-arc-pro-mem-wb-0.15M-sim-7.nc4mqs-arc-pro-mem-wb-0.15M-sim-8.nc4mqs-arc-pro-mem-wb-0.15M-sim-9.nc4mqs-arc-pro-mem-wb-0.15M-sim-10.nc4mqs-ixo-pro-mem-wb-0.15M-sim-1.nc4mqs-ixo-pro-mem-wb-0.15M-sim-2.nc4mqs-ixo-pro-mem-wb-0.15M-sim-3.nc4mqs-ixo-pro-mem-wb-0.15M-sim-4.nc4mqs-ixo-pro-mem-wb-0.15M-sim-5.nc4mqs-ixo-pro-mem-wb-0.15M-sim-6.nc4mqs-ixo-pro-mem-wb-0.15M-sim-7.nc4mqs-ixo-pro-mem-wb-0.15M-sim-8.nc4mqs-ixo-pro-mem-wb-0.15M-sim-9.nc4mqs-ixo-pro-mem-wb-0.15M-sim-10.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-1.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-2.nc4mqs-nb-arc-pro-mem-wb-0.15M-sim-3.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-1.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-2.nc4mqs-nb-ixo-pro-mem-wb-0.15M-sim-3.nc stride: 100 ps / frame * PSF/PDB files for loading the trajectories:3uon-apo-c36-pro-mem-wb-0.15M-pro.pdb3uon-apo-c36-pro-mem-wb-0.15M-pro.psf3uon-c36-pro-mem-wb-0.15M-pro.pdb3uon-c36-pro-mem-wb-0.15M-pro.psf4mqs-apo-pro-mem-wb-0.15M-pro.pdb4mqs-apo-pro-mem-wb-0.15M-pro.psf4mqs-arc-pro-mem-wb-0.15M-pro.pdb4mqs-arc-pro-mem-wb-0.15M-pro.psf4mqs-ixo-pro-mem-wb-0.15M-pro.pdb4mqs-ixo-pro-mem-wb-0.15M-pro.psf4mqs-nb-arc-pro-mem-wb-0.15M-pro.pdb4mqs-nb-arc-pro-mem-wb-0.15M-pro.psf4mqs-nb-ixo-pro-mem-wb-0.15M-pro.pdb4mqs-nb-ixo-pro-mem-wb-0.15M-pro.psf

* 本数据集的模拟实验基于以下论文：Miao Y与McCammon JA（2016）《毒蕈碱型G蛋白偶联受体（G-protein–coupled receptor, GPCR）的分级激活与自由能景观》，发表于《美国国家科学院院刊》，卷113，第43期，页码12162–12167，PMCID编号：PMC5087018。 * 模拟时长： 1. 系统4mqs-apo-pro-mem-wb-0.15M：共3次重复模拟（模拟编号1、2、3），时长分别为410 ns、460 ns、430 ns 2. 系统3uon-apo-c36-pro-mem-wb-0.15M：共3次重复模拟（模拟编号1、2、3），时长均为400 ns 3. 系统3uon-c36-pro-mem-wb-0.15M：共3次重复模拟（模拟编号1、2、3），时长分别为405 ns、405 ns、400 ns 4. 系统4mqs-nb-arc-pro-mem-wb-0.15M：共3次重复模拟（模拟编号1、2、3），时长分别为402 ns、405 ns、400 ns 5. 系统4mqs-nb-ixo-pro-mem-wb-0.15M：共3次重复模拟（模拟编号顺序为1、3、2），时长分别为500 ns、400 ns、500 ns 6. 系统4mqs-arc-pro-mem-wb-0.15M：共10次重复模拟（模拟编号1~10），时长分别为2030 ns、1520 ns、1190 ns、650 ns、650 ns、650 ns、620 ns、600 ns、600 ns、540 ns 7. 系统4mqs-ixo-pro-mem-wb-0.15M：共10次重复模拟（模拟编号1~10），时长分别为1050 ns、1000 ns、940 ns、500 ns、500 ns、500 ns、500 ns、480 ns、450 ns、410 ns * 模拟轨迹文件清单： 3uon-c36-pro-mem-wb-0.15M-sim-1.nc 3uon-c36-pro-mem-wb-0.15M-sim-2.nc 3uon-c36-pro-mem-wb-0.15M-sim-3.nc 4mqs-arc-pro-mem-wb-0.15M-sim-1.nc 4mqs-arc-pro-mem-wb-0.15M-sim-2.nc 4mqs-arc-pro-mem-wb-0.15M-sim-3.nc 4mqs-arc-pro-mem-wb-0.15M-sim-4.nc 4mqs-arc-pro-mem-wb-0.15M-sim-5.nc 4mqs-arc-pro-mem-wb-0.15M-sim-6.nc 4mqs-arc-pro-mem-wb-0.15M-sim-7.nc 4mqs-arc-pro-mem-wb-0.15M-sim-8.nc 4mqs-arc-pro-mem-wb-0.15M-sim-9.nc 4mqs-arc-pro-mem-wb-0.15M-sim-10.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-1.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-2.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-3.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-4.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-5.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-6.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-7.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-8.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-9.nc 4mqs-ixo-pro-mem-wb-0.15M-sim-10.nc 4mqs-nb-arc-pro-mem-wb-0.15M-sim-1.nc 4mqs-nb-arc-pro-mem-wb-0.15M-sim-2.nc 4mqs-nb-arc-pro-mem-wb-0.15M-sim-3.nc 4mqs-nb-ixo-pro-mem-wb-0.15M-sim-1.nc 4mqs-nb-ixo-pro-mem-wb-0.15M-sim-2.nc 4mqs-nb-ixo-pro-mem-wb-0.15M-sim-3.nc * 轨迹帧步长：每帧间隔100 ps * 用于加载轨迹的蛋白质结构文件（Protein Structure File, PSF）与蛋白质数据库格式文件（Protein Data Bank, PDB）： 3uon-apo-c36-pro-mem-wb-0.15M-pro.pdb 3uon-apo-c36-pro-mem-wb-0.15M-pro.psf 3uon-c36-pro-mem-wb-0.15M-pro.pdb 3uon-c36-pro-mem-wb-0.15M-pro.psf 4mqs-apo-pro-mem-wb-0.15M-pro.pdb 4mqs-apo-pro-mem-wb-0.15M-pro.psf 4mqs-arc-pro-mem-wb-0.15M-pro.pdb 4mqs-arc-pro-mem-wb-0.15M-pro.psf 4mqs-ixo-pro-mem-wb-0.15M-pro.pdb 4mqs-ixo-pro-mem-wb-0.15M-pro.psf 4mqs-nb-arc-pro-mem-wb-0.15M-pro.pdb 4mqs-nb-arc-pro-mem-wb-0.15M-pro.psf 4mqs-nb-ixo-pro-mem-wb-0.15M-pro.pdb 4mqs-nb-ixo-pro-mem-wb-0.15M-pro.psf

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创建时间：

2019-03-01