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用于蛋白质溶剂可及性预测和最近邻效应分析的查找表。

Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis.

作者信息

Wang Jung-Ying, Ahmad Shandar, Gromiha M Michael, Sarai Akinori

机构信息

Department of Multimedia and Game Science, Lunghwa University of Science and Technology, Taoyuan, Taiwan.

出版信息

Biopolymers. 2004 Oct 15;75(3):209-16. doi: 10.1002/bip.20113.

Abstract

We developed dictionaries of two-, three-, and five-residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look-up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that predictions made in this way are very close to those made using more sophisticated methods of solvent accessibility prediction. We also analyzed the effect of immediate neighbors on the solvent accessibility of residues. This helps us in understanding how the same residue type may have different accessible surface areas in different proteins and in different positions of the same protein. We observe that certain residues have a tendency to increase or decrease the solvent accessibility of their neighboring residues in C- or N-terminal positions. Interestingly, the C-terminal and N-terminal neighbor residues are found to have asymmetric roles in modifying solvent accessibility of residues. As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look-up tables are provided on the web at www.netasa.org/look-up/.

摘要

我们开发了蛋白质中两残基、三残基和五残基模式的字典,并计算了其天然蛋白质中中心残基的平均溶剂可及性。这些字典可作为查找表,用于后续预测氨基酸残基的溶剂可及性。我们发现,以这种方式做出的预测与使用更复杂的溶剂可及性预测方法做出的预测非常接近。我们还分析了紧邻残基对残基溶剂可及性的影响。这有助于我们理解相同的残基类型在不同蛋白质以及同一蛋白质的不同位置如何具有不同的可及表面积。我们观察到,某些残基倾向于增加或降低其C端或N端位置相邻残基的溶剂可及性。有趣的是,发现C端和N端相邻残基在修饰残基的溶剂可及性方面具有不对称作用。正如预期的那样,相似的相邻残基会增强残基的疏水或亲水特性。详细的查找表可在网站www.netasa.org/look-up/上获取。

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