Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

This is the "parent" repository for the Data Note : "­Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli. It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it. It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one. Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study. Description of files in this dataset: <strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10. <strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2. Details of how this data was produced is available in the Abelak_etal_Methods.docx document.本数据集为Abelak、Bishop-Bailey与Nobeli所著数据笔记《野生型与突变型人CYP2J2与多不饱和脂肪酸相互作用的分子动力学模拟》的“父级”存储库。该存储库包含一份文档（<strong>Abelak_etal_Methods.pdf</strong>），用于说明生成本数据集及所有配套存储库中数据所采用的研究方法。此外还包含一个Shell脚本（<strong>create_sim4_repeats.sh</strong>），该脚本是本项目配套存储库中用于搭建分子动力学模拟环境的典型脚本。最后，本数据集还包含同源建模与分子对接模拟的结果，这些结果作为本研究中分子动力学模拟的初始起点。本数据集内的文件说明如下：<strong>C2J2_min3_mod_noH.pdb</strong>：野生型CYP2J2的同源建模结构，其构建基于以蛋白质数据库（Protein Data Bank，PDB）编号1SUO、2P85、3EBS及1Z10为模板的序列比对。<strong>docking_wild_type_C2J2.zip</strong>：9个与野生型CYP2J2同源建模结构对接的花生四烯酸构象结果，该数据的生成细节可参阅<strong>Abelak_etal_Methods.docx</strong>文档。