PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations.

J Chem Inf Model

Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de Mexico 09340, Mexico.

Published: April 2021

AI Article Synopsis

  • The secondary structure is crucial for analyzing, classifying, and modeling proteins, and a new method called PSIQUE has been developed for more accurate secondary structure assignment.
  • PSIQUE utilizes the potential energy surface (PES) of polyalanine through density functional theory to identify uniform protein segments and secondary structure motifs based on energy minima.
  • This method outperforms existing techniques by better distinguishing subtle secondary structures and producing more uniform segments while accommodating local distortions, making it effective for detailed protein characterization.

Article Abstract

The secondary structure is important in protein structure analysis, classification, and modeling. We have developed a novel method for secondary structure assignment, termed PSIQUE, based on the potential energy surface (PES) of polyalanine obtained using an infinitely long chain model and density functional theory calculations. First, uniform protein segments are determined in terms of a difference of quaternions between neighboring amino acids along the protein backbone. Then, the identification of the secondary structure motifs is carried out based on the minima found in the PES. PSIQUE shows good agreement with other secondary structure assignment methods. However, it provides better discrimination of subtle secondary structures (, helix types) and termini and produces more uniform segments while also accounting for local distortions. Overall, PSIQUE provides a precise and reliable assignment of secondary structures, so it should be helpful for the detailed characterization of the protein structure.

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Source
http://dx.doi.org/10.1021/acs.jcim.0c01343DOI Listing

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