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Current Proteomics

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ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

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Research Article

Protein Secondary Structure Determination (PSSD): A New and Simple Approach

Author(s): Anindya Sundar Panja, Bidyut Bandopadhyay, Akash Nag and Smarajit Maiti*

Volume 16, Issue 3, 2019

Page: [246 - 253] Pages: 8

DOI: 10.2174/1570164615666180911113251

Price: $65

Abstract

Background: Our present investigation was conducted to explore the computational algorithm for the protein secondary structure prediction as per the property of evolutionary transient and large number (each 50) of homologous mesophilic-thermophilic proteins.

Objectives: These mesophilic-thermophilic proteins were used for numerical measurement of helix-sheetcoil and turn tendency for which each amino-acid residue is screened to build up the propensity-table.

Methods: In the current study, two different propensity windows have been introduced that allowed predicting the secondary structure of protein more than 80% accuracy.

Results: Using this propensity matrix and dynamic algorithm-based programme, a significant and decisive outcome in the determination of protein (both thermophilic and mesophilic) secondary structure was noticed over the previous algorithm based programme. It was demonstrated after comparison with other standard methods including DSSP adopted by PDB with the help of multiple comparisons ANOVA and Dunnett’s t-test.

Conclusion: The PSSD is of great importance in the prediction of structural features of any unknown, unresolved proteins. It is also useful in the studies of proteins structure-function relationship.

Keywords: PSSD and DSSP, GOR and Chou Fasman algorithm, thermophilic and mesophilic proteins, propensity matrix, helix sheet and turn, statistics.

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