【分子对接学习】PDB怎么选择对接的蛋白质结构20220602

2022-06-02 21:12 作者:菜鸟博士_杂货铺 0人读过 | 我要投稿

【分子对接】PDB怎么选择对接的蛋白质结构20220602

菜鸟博士学习

生物大分子 3D 结构的合理选择，用于内分泌干扰物作用机制的分子对接研究。 分子建模已成为预测和模拟化学物质内分泌干扰作用的重要工具。成功应用分子建模的一个关键先决条件是要模拟的生物大分子的 3D 结构的正确性。迄今为止，有几个数据库可以提供实验确定的 3D 结构。然而，通常存在许多挑战或不利因素，例如，(a) 蛋白质数据库中给定生物大分子目标的大量 3D 结构；(b) 这些结构的质量可变性；(c) 属于不同的物种；(d) 关键位置的突变氨基酸残基，等等。一旦在分子建模中选择了不合适的目标生物大分子的 3D 结构，建模结果的准确性和科学性不可避免地受到影响。在本文中，基于文献调查和蛋白质数据库中属于内分泌系统的生物大分子靶标的 3D 结构表征的分析，提出了六个原则来指导选择合适的生物大分子 3D 结构。原则包括考虑物种多样性、作用机制、是否存在突变氨基酸残基、蛋白链数是否正确、3D结构中的配体与目标化合物的结构相似程度等因素，例如，结构的实验pH条件决定了过程和分辨率。基于文献调查和蛋白质数据库中属于内分泌系统的生物大分子靶标的 3D 结构特征分析，提出了六项原则来指导选择合适的生物大分子 3D 结构。原则包括考虑物种多样性、作用机制、是否存在突变氨基酸残基、蛋白链数是否正确、3D结构中的配体与目标化合物的结构相似程度等因素，例如，结构的实验pH条件决定了过程和分辨率。基于文献调查和蛋白质数据库中属于内分泌系统的生物大分子靶标的 3D 结构特征分析，提出了六项原则来指导选择合适的生物大分子 3D 结构。原则包括考虑物种多样性、作用机制、是否存在突变氨基酸残基、蛋白链数是否正确、3D结构中的配体与目标化合物的结构相似程度等因素，例如，结构的实验pH条件决定了过程和分辨率。

Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action.

Chemical Research in Toxicology(IF3.739)Pub Date : 2016-08-25, DOI:10.1021/acs.chemrestox.6b00245

Xianhai Yang1, Huihui Liu2, Jining Liu1, Fei Li3, Xuehua Li4, Lili Shi1, Jingwen Chen4

Affiliation

Molecular modeling has become an essential tool in predicting and simulating endocrine disrupting effects of chemicals. A key prerequisite for successful application of molecular modeling lies in the correctness of 3D structure for biomacromolecules to be simulated. To date, there are several databases that can provide the experimentally-determined 3D structures. However, commonly, there are many challenges or disadvantageous factors, e.g., (a) lots of 3D structures for a given biomacromolecular target in the protein database; (b) the quality variability for those structures; (c) belonging to different species; (d) mutant amino acid residue in key positions, and so on. Once an inappropriate 3D structure of a target biomacromolecule was selected in molecular modeling, the accuracy and scientific nature of the modeling results could be inevitably affected. In this article, based on literature survey and an analysis of the 3D structure characterization of biomacromolecular targets belonging to the endocrine system in protein databases, six principles were proposed to guide the selection of the appropriate 3D structure of biomacromolecules. The principles include considering the species diversity, the mechanism of action, whether there are mutant amino acid residues, whether the number of protein chains is correct, the degree of structural similarity between the ligand in 3D structure and the target compounds, and other factors, e.g., the experimental pH conditions of the structure determined process and resolution.