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

## TL;DR

A new tool called PepString helps researchers find short amino acid sequences in proteins, which could be important for understanding Alzheimer's disease.

## Contribution

PepString is the first tool for efficiently searching short (≥3) amino acid subsequences in public protein databases.

## Key findings

- PepString enables intuitive queries to find proteins containing specific short subsequences.
- The tool was demonstrated by identifying the EVHH tetrapeptide linked to Alzheimer’s disease.
- Current tools lack the ability to efficiently search for short amino acid sequences.

## 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.