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Title

SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2

 

Authors

Parth Sarthi Sen Gupta+, Arnab Nayek+, Shyamashree Banerjee+, Pratyay Seth, Sunit Das, Vishma Pratap Sur, Chittran Roy & Amal Kumar Bandyopadhyay*

 

Affiliation

Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104

 

Email

akbanerjee@biotech.buruniv.ac.in; *Corresponding author

 

Article Type

Software

 

Date

Received December 14, 2014; Accepted December 25, 2014; Published January 30, 2015

 

Abstract

Specific electrostatics (i.e. salt-bridge) includes both local and non-local interactions that contribute to the overall stability of proteins. It has been shown that a salt-bridge could either be buried or exposed, networked or isolated, hydrogen-bonded or non-hydrogen bonded, in secondary-structure or in coil, formed by single or multiple bonds. Further it could also participates either in intra- or inter-dipole interactions with preference in orientation either for basic residue at N-terminal (orientation-I) or acidic residue at N-terminal (orientation-II). In this context SBION2 is unique in that it reports above mentioned binary items in excel format along with details on intra and inter-dipole interactions and orientations. These results are suitable for post run statistical analyses involving large datasets. Reports are also made on protein-protein interactions, intervening residue distances and general residue specific salt-bridge details. A ready to use compact supplementary table is also produced. The program runs in three alternative modes. Each mode works on any number of structure files with any number of chains at any given atomic distance of ion-pair. Thus SBION2 provides intricate details on salt-bridges and finds application in structural bioinformatics.

 

Availability

SBION2 is freely available at http://sourceforge.net/projects/sbion2/ for academic users.

 

Keywords

salt-bridge, intra helical, bond multiplicity, core, surface, networked, isolated

 

Citation

Gupta et al. Bioinformation 11(1): 039-042 (2015)

 

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.