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 different enzymes and their corresponding model substrates using molecular docking software. First, structural data of target enzymes were obtained via methods including PDB database search, enzyme molecular crystallization, and X-ray diffraction. The 3D structures of small molecules such as substrates and cofactors were drawn using ChemDraw software. During the docking process, 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 recorded in the obtained .dlg files. Appropriate structures were selected for subsequent analytical experiments by comprehensively considering factors such as 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

该数据集是一个基于计算模拟的酶-底物分子对接数据集，通过分子对接软件分析酶与模式底物的相互作用，包括结合能、氢键等关键因素评估。数据集由华东理工大学创建，数据量为26.3MB，来源于国家重点研发计划项目，适用于生物化学工程领域的研究。