Dataset (II) related to publication: Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors
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MD simulation data of <strong>1</strong> related to the publication Pantsar et al.: <em>Decisive Role of Water and Protein Dynamics in Residence Time of p38a MAP Kinase Inhibitors.</em> Individual .zip files contain raw-desmond trajectories (-out.cms files and trj-files). All datasets related to this publication: https://doi.org/10.5281/zenodo.4568113(compound <strong>1</strong>; dataset: I) https://doi.org/10.5281/zenodo.4572444 (compound <strong>1</strong>; dataset: II) https://doi.org/10.5281/zenodo.4561797(compound <strong>2</strong>; dataset: III) https://doi.org/10.5281/zenodo.4563896 (compound <strong>2</strong>; dataset: IV) https://doi.org/10.5281/zenodo.5563359 (<strong>SB203580</strong>; dataset: V) https://doi.org/10.5281/zenodo.5563655 (<strong>SB203580</strong>; dataset: VI) https://doi.org/10.5281/zenodo.5564118 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VII) https://doi.org/10.5281/zenodo.5564208 (compound <strong>1</strong> simulated in compound <strong>2</strong> metastable state <strong>2-<em>S</em><sub>3</sub></strong>; dataset: VIII) https://doi.org/10.5281/zenodo.5564586 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: IX) https://doi.org/10.5281/zenodo.5570882 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: X) https://doi.org/10.5281/zenodo.5571352 (well-tempered metadynamics simulations of compounds <strong>1</strong> and <strong>2</strong>; dataset: XI) The datasets include original Desmond raw-trajectories (datasets I–VIII), PDB-coordinates for the energy minimized metastable state derived structures (datasets II, IV and VI) and raw-trajectories of the well-tempered metadynamics simulations (dataset IX–XI).
本数据集为与Pantsar等人发表的论文《水与蛋白质动力学对p38α丝裂原活化蛋白激酶（p38a MAP Kinase）抑制剂驻留时间的决定性作用》相关的**1号化合物**的分子动力学（Molecular Dynamics, MD）模拟数据。单个.zip压缩包均包含原始Desmond轨迹文件（-out.cms文件与trj轨迹文件）。 本论文相关的全部数据集如下： https://doi.org/10.5281/zenodo.4568113（化合物1；数据集I） https://doi.org/10.5281/zenodo.4572444（化合物1；数据集II） https://doi.org/10.5281/zenodo.4561797（化合物2；数据集III） https://doi.org/10.5281/zenodo.4563896（化合物2；数据集IV） https://doi.org/10.5281/zenodo.5563359（SB203580；数据集V） https://doi.org/10.5281/zenodo.5563655（SB203580；数据集VI） https://doi.org/10.5281/zenodo.5564118（在化合物2亚稳态2-S₃中模拟的化合物1；数据集VII） https://doi.org/10.5281/zenodo.5564208（在化合物2亚稳态2-S₃中模拟的化合物1；数据集VIII） https://doi.org/10.5281/zenodo.5564586（化合物1与化合物2的适度恒温元动力学（well-tempered metadynamics）模拟数据；数据集IX） https://doi.org/10.5281/zenodo.5570882（化合物1与化合物2的适度恒温元动力学模拟数据；数据集X） https://doi.org/10.5281/zenodo.5571352（化合物1与化合物2的适度恒温元动力学模拟数据；数据集XI） 本批数据集包含原始Desmond轨迹文件（数据集I~VIII）、由能量最小化亚稳态结构得到的PDB（Protein Data Bank）坐标文件（数据集II、IV与VI），以及适度恒温元动力学模拟的原始轨迹文件（数据集IX~XI）。
