【分子對(duì)接】PDB怎么選擇對(duì)接的蛋白質(zhì)結(jié)構(gòu)20220602

菜鳥博士學(xué)習(xí)

生物大分子 3D 結(jié)構(gòu)的合理選擇，用于內(nèi)分泌干擾物作用機(jī)制的分子對(duì)接研究。?分子建模已成為預(yù)測(cè)和模擬化學(xué)物質(zhì)內(nèi)分泌干擾作用的重要工具。成功應(yīng)用分子建模的一個(gè)關(guān)鍵先決條件是要模擬的生物大分子的 3D 結(jié)構(gòu)的正確性。迄今為止，有幾個(gè)數(shù)據(jù)庫(kù)可以提供實(shí)驗(yàn)確定的 3D 結(jié)構(gòu)。然而，通常存在許多挑戰(zhàn)或不利因素，例如，(a) 蛋白質(zhì)數(shù)據(jù)庫(kù)中給定生物大分子目標(biāo)的大量 3D 結(jié)構(gòu)；(b) 這些結(jié)構(gòu)的質(zhì)量可變性；(c) 屬于不同的物種；(d) 關(guān)鍵位置的突變氨基酸殘基，等等。一旦在分子建模中選擇了不合適的目標(biāo)生物大分子的 3D 結(jié)構(gòu)，建模結(jié)果的準(zhǔn)確性和科學(xué)性不可避免地受到影響。在本文中，基于文獻(xiàn)調(diào)查和蛋白質(zhì)數(shù)據(jù)庫(kù)中屬于內(nèi)分泌系統(tǒng)的生物大分子靶標(biāo)的 3D 結(jié)構(gòu)表征的分析，提出了六個(gè)原則來(lái)指導(dǎo)選擇合適的生物大分子 3D 結(jié)構(gòu)。原則包括考慮物種多樣性、作用機(jī)制、是否存在突變氨基酸殘基、蛋白鏈數(shù)是否正確、3D結(jié)構(gòu)中的配體與目標(biāo)化合物的結(jié)構(gòu)相似程度等因素，例如，結(jié)構(gòu)的實(shí)驗(yàn)pH條件決定了過程和分辨率?；谖墨I(xiàn)調(diào)查和蛋白質(zhì)數(shù)據(jù)庫(kù)中屬于內(nèi)分泌系統(tǒng)的生物大分子靶標(biāo)的 3D 結(jié)構(gòu)特征分析，提出了六項(xiàng)原則來(lái)指導(dǎo)選擇合適的生物大分子 3D 結(jié)構(gòu)。原則包括考慮物種多樣性、作用機(jī)制、是否存在突變氨基酸殘基、蛋白鏈數(shù)是否正確、3D結(jié)構(gòu)中的配體與目標(biāo)化合物的結(jié)構(gòu)相似程度等因素，例如，結(jié)構(gòu)的實(shí)驗(yàn)pH條件決定了過程和分辨率。基于文獻(xiàn)調(diào)查和蛋白質(zhì)數(shù)據(jù)庫(kù)中屬于內(nèi)分泌系統(tǒng)的生物大分子靶標(biāo)的 3D 結(jié)構(gòu)特征分析，提出了六項(xiàng)原則來(lái)指導(dǎo)選擇合適的生物大分子 3D 結(jié)構(gòu)。原則包括考慮物種多樣性、作用機(jī)制、是否存在突變氨基酸殘基、蛋白鏈數(shù)是否正確、3D結(jié)構(gòu)中的配體與目標(biāo)化合物的結(jié)構(gòu)相似程度等因素，例如，結(jié)構(gòu)的實(shí)驗(yàn)pH條件決定了過程和分辨率。

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.

篩選步驟：

物種：

Homo sapiens

分辨率：2.5?以下

refine

Tabular report：

勾選選項(xiàng)：PBD ID ligand配體 Value; pH; EM resolution分辨率

Run report

下載運(yùn)行報(bào)告進(jìn)行篩選

使用配體與蛋白進(jìn)行對(duì)接，驗(yàn)證可靠性。