Universität zu Köln

Milchevskaya, Vladislava ORCID: 0000-0002-4350-8424, Nikitin, Alexei M., Lukshin, Sergey A., Filatov, Ivan V., Kravatsky, Yuri V., Tumanyan, Vladimir G., Esipova, Natalia G. and Milchevskiy, Yury V. (2021). Structural coordinates: A novel approach to predict protein backbone conformation. PLoS One, 16 (5). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

Full text not available from this repository.

Abstract

Motivation Local protein structure is usually described via classifying each peptide to a unique class from a set of pre-defined structures. These classifications may differ in the number of structural classes, the length of peptides, or class attribution criteria. Most methods that predict the local structure of a protein from its sequence first rely on some classification and only then proceed to the 3D conformation assessment. However, most classification methods rely on homologous proteins' existence, unavoidably lose information by attributing a peptide to a single class or suffer from a suboptimal choice of the representative classes. Results To alleviate the above challenges, we propose a method that constructs a peptide's structural representation from the sequence, reflecting its similarity to several basic representative structures. For 5-mer peptides and 16 representative structures, we achieved the Q16 classification accuracy of 67.9%, which is higher than what is currently reported in the literature. Our prediction method does not utilize information about protein homologues but relies only on the amino acids' physicochemical properties and the resolved structures' statistics. We also show that the 3D coordinates of a peptide can be uniquely recovered from its structural coordinates, and show the required conditions under various geometric constraints.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Milchevskaya, Vladislava UNSPECIFIED orcid.org/0000-0002-4350-8424 UNSPECIFIED Nikitin, Alexei M. UNSPECIFIED UNSPECIFIED UNSPECIFIED Lukshin, Sergey A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Filatov, Ivan V. UNSPECIFIED UNSPECIFIED UNSPECIFIED Kravatsky, Yuri V. UNSPECIFIED UNSPECIFIED UNSPECIFIED Tumanyan, Vladimir G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Esipova, Natalia G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Milchevskiy, Yury V. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-583525
DOI:	10.1371/journal.pone.0239793
Journal or Publication Title:	PLoS One
Volume:	16
Number:	5
Date:	2021
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RELATE 2 SETS; SECONDARY STRUCTURE; ROTATION Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/58352