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Title |
SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files
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Authors |
Parth Sarthi Sen Gupta1, Sudipta Mondal1, Buddhadev Mondal2, Rifat Nawaz Ul Islam1, Shyamashree Banerjee1 & Amal K Bandyopadhyay1*
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Affiliation |
1Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India; 2Department of Zoology, Burdwan Raj College, The University of Burdwan, Golapbag, Burdwan, 713104, West Bengal, India |
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akbanerjee@biotech.buruniv.ac.in; *Corresponding authors
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Article Type |
Software
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Date |
Received February 11, 2014; Revised February 24, 2014; Accepted February 25, 2014; Published March 19, 2014
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Abstract |
Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges. While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION which can perform all the above mentioned computations for any number of protein with any number of chain at any given distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses potential for applications in the field of structural and comparative bioinformatics studies.
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Availability |
: SBION is freely available for non-commercial/academic institutions on formal request to the corresponding author (akbanerjee@biotech.buruniv.ac.in).
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Keywords |
UNIX; physicochemical properties; FASTA; software; protein sequence.
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Citation |
Gupta et al.
Bioinformation 10(03): 164-166 (2014) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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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. |