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Title

PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins

 

Authors

Rifat Nawaz UL Islam1#, Chittran Roy2#, Parth Sarthi Sen Gupta3#, Shyamashree Banerjee2#, Debanjan Mitra2#, Sahini Banerjee4#, Amal Kumar Bandyopadhyay2#*

 

Affiliation

1Department of Zoology, The University of Burdwan, West Bengal, 713104, India;

2Department of Biotechnology, The University of Burdwan, West Bengal, 713104, India;

3Department of Chemistry, IISER Berhampur, Berhampur, Odisha, 760010, India;

4Department of Biotechnology, Institute of Genetic Engineering, West Bengal, 700128, India;

 

Email

akbanerjee@biotech.buruniv.ac.in

 

Article Type

Software

 

Date

Received May 6, 2018; Revised May 8, 2018; Accepted May 8, 2018; Published May 31, 2018;

 

Abstract

Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical procedure. It also classifies them in range specific and chain specific manners. It further computes percentage composition and physicochemical properties along with residues propensities. It also prepares FASTA files for different segments (helix, strand and coil) in the exact order that they follow in the sequence. Representative analyses on orthologous (homologous across species) proteins demonstrate wide segmental variations of physicochemical properties. Such variations provide insights to relate the adaptation of these proteins in a given functional constraint under diverse environmental conditions. Thus, the program finds applications in the structural and evolutionary analysis of proteins.

 

Keywords

Protein, Chou and Fasman, propensity, properties, Program, secondary structure

 

Citation

Islam et al. Bioinformation 14(5): 190-193 (2018)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.