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  3. Volume 15, 2024
  4. Method for Recognizing the Characteristic Elements of Protein Secondary Structure From the Llm of Its Amino Acid Sequence

Method for Recognizing the Characteristic Elements of Protein Secondary Structure From the Llm of Its Amino Acid Sequence

SISN.
2024;
Volume 15
: pp. 460 - 468
https://doi.org/10.23939/sisn2024.15.460
Authors:
  1. Yaroslav Teplyi
1
Lviv Polytechnic National University, ISN, Lviv, Ukraine

The spatial structure of a protein determines its biochemical properties and, consequently, its function. The same applies to elements of secondary structure, which adopt shapes of helices, coiled coils, strands, sheets and other formations in three-dimensional space. Automatic detection of such formations based on their corresponding amino acid sequences in the protein will enable the cataloging of these sequence fragments, examining and systematizing their correspondence to spatial protein formations. This, in turn, should simplify the task of searching for complementary and functional similarities among different proteins. For this purpose, a method based on covariance, autocorrelation, and spatial-spectral analysis of embeddings of their amino acid sequences has been developed and tested.

protein structure prediction
ESM-2 model
embeddings
autocorrelation analysis
protein secondary structure
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