Title: CoSec: a hub of online tools for comparing secondary structure elements

Authors: Ankur Chaurasia; Jyotilipsa Mohanty; Lukkani Laxman Kumar; Ayaluru Murali

Addresses: Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry – 605 014, India ' Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry – 605 014, India ' Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry – 605 014, India ' Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry – 605 014, India

Abstract: A common problem with in-silico protein modelling is choosing the best model out of a cluster of protein models suggested by the online servers. Besides identifying a right model based on torsion angles and potentials, a lot of researchers look at the model that retains most of its predicted secondary structures. The comparison of the secondary structure elements at residue level becomes more tedious as the size of the protein increases. So, we have developed two tools predicted secondary structure matching (PreSSM) and compare assigned secondary structure (CompASS) under one umbrella CoSec. PreSSM compares the secondary structure elements of a modelled protein from a PDB to the secondary structure predicted, while CompASS compares the secondary structures between two PDBs of the same protein (typically the models before and after simulation/docking with a ligand/mutation). Moreover, the two tools use STRIDE (with 95% consensus, with 5% divergence) to assign secondary structure confirmation to residues in the given protein's structure.

Keywords: bioinformatics; computational biology; secondary structure analysis; sequence analysis; protein structure; molecular dynamic simulation.

DOI: 10.1504/IJBRA.2023.131275

International Journal of Bioinformatics Research and Applications, 2023 Vol.19 No.1, pp.56 - 69

Received: 11 Nov 2022
Accepted: 04 Jan 2023
Published online: 05 Jun 2023 *