Title

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

Authors

Rifat Nawaz UL Islam^1#, Chittran Roy^2#, Parth Sarthi Sen Gupta^3#, Shyamashree Banerjee^2#, Debanjan Mitra^2#, Sahini Banerjee^4#, Amal Kumar Bandyopadhyay^2#*

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;

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.