酶-底物结构分子对接数据集

采用分子对接软件对不同酶与对应模式底物的分子对接模拟分析，首先通过PDB数据库搜索、酶分子结晶并通过X射线衍射等方法获得目标酶的结构数据，通过chemdraw软件绘制底物、辅因子等小分子的3D结构，对接时依次将辅因子和酶对接到酶的活性口袋中，设置对接区域为30×30×30，区域内涵盖酶的关键催化残基。运行软件后，对获得的dlg文件中包含的底物及辅因子等小分子结构在酶活性口袋中的不同结合形态进行分析，结合考虑酶-小分子之间结合能、氢键、关键原子间距等因素选择合适的结构进行后续的分析实验。Molecular docking simulation analysis was conducted on various enzymes and their corresponding model substrates using molecular docking software. First, structural data of target enzymes were obtained through methods including PDB database searching, enzyme crystallization, and X-ray diffraction. The 3D structures of small molecules such as substrates and cofactors were drawn using ChemDraw software. During the docking procedure, cofactors and enzymes were sequentially docked into the active pockets of the enzymes, with the docking region set to 30×30×30, which covers the key catalytic residues of the enzymes. After running the software, analysis was performed on the distinct binding conformations of small molecules including substrates and cofactors within the enzyme active pockets, as stored in the acquired .dlg files. Appropriate structures were selected for subsequent analytical experiments by considering factors such as the binding energy, hydrogen bonds, and key atomic distances between enzymes and small molecules.

搜集汇总

背景与挑战

背景概述

该数据集是一个酶-底物结构分子对接数据集，专注于化学工程领域，通过分子对接软件模拟酶与模式底物的相互作用。它包含从PDB数据库获取的酶结构数据、chemdraw绘制的底物3D结构，以及对接分析结果，考虑结合能、氢键等关键因素，适用于酶催化机制研究。数据集由华东理工大学所有，通过国家基础学科公共科学数据中心完全共享，需在线申请获取。