PepString Server As a Tool to Search for Short Amino Acid Subsequences: Identification of Potential Amyloid-Beta Targets.

IF 2 4区生物学 Q4 CELL BIOLOGY

Acta Naturae Pub Date : 2025-07-01 DOI:10.32607/actanaturae.27630

S A Kozin, A A Anashkina, D G Matsuga, B S Suvaan, V G Tumanyan, V A Mitkevich, A A Makarov

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Abstract

This paper presents a new bioinformatics tool to meet the needs of researchers in the search for short (≥ 3) amino acid subsequences in protein sequences annotated in public databases (UniprotKB, SwissProt) and illustrates its efficacy with the example of a search for the EVHH tetrapeptide in the human proteome, which is a molecular determinant of amyloid beta and is involved in interactions that are crucial in Alzheimer's disease pathogenesis. The topicality of developing such a tool is, on the one hand, supported by experimental data on the role of short tetrapeptide motifs in the architecture of intermolecular interfaces. On the other hand, there are currently no software products for efficient search for short (≥3) amino acid sequences in public databases, which drastically limits researchers' ability to identify proteins with exact matches of short subsequences. This tool (PepString server, http://pepstring.eimb.ru/) allows one to use intuitive queries to retrieve information about all the proteins that contain sequences of interest, as well as their combinations.

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PepString服务器作为搜索短氨基酸子序列的工具：鉴定潜在的β淀粉样蛋白靶点。

本文提出了一种新的生物信息学工具，以满足研究人员在公共数据库（UniprotKB, SwissProt）中注释的蛋白质序列中寻找短（≥3）氨基酸子序列的需求，并以人类蛋白质组中EVHH四肽的搜索为例说明了其有效性，EVHH四肽是淀粉样蛋白的分子决定因素，参与阿尔茨海默病发病机制中至关重要的相互作用。开发这种工具的话题性一方面是由短四肽基序在分子间界面结构中的作用的实验数据支持的。另一方面，目前还没有能够在公共数据库中高效搜索短（≥3）氨基酸序列的软件产品，这极大地限制了研究人员识别具有短子序列精确匹配的蛋白质的能力。这个工具（PepString服务器，http://pepstring.eimb.ru/）允许人们使用直观的查询来检索包含感兴趣序列的所有蛋白质的信息，以及它们的组合。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Acta Naturae 农林科学-林学

CiteScore

3.50

自引率

5.00%

发文量

审稿时长

>12 weeks

期刊介绍： Acta Naturae is an international journal on life sciences based in Moscow, Russia. Our goal is to present scientific work and discovery in molecular biology, biochemistry, biomedical disciplines and biotechnology. These fields represent the most important priorities for the research and engineering development both in Russia and worldwide. Acta Naturae is also a periodical for those who are curious in various aspects of biotechnological business, innovations in pharmaceutical areas, intellectual property protection and social consequences of scientific progress. The journal publishes analytical industrial surveys focused on the development of different spheres of modern life science and technology. Being a radically new and totally unique journal in Russia, Acta Naturae is useful to both representatives of fundamental research and experts in applied sciences.