title: SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2.
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 nonhydrogen 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.
  
  
  BACKGROUND
  SBION2 is freely available at http://sourceforge.net/projects/sbion2/ for academic users.
authors.affiliation: Authors equally contributed.
authors.forename: Parth Sarthi Sen
authors.initials: PS
authors.lastname: Gupta
authors.affiliation: Authors equally contributed.
authors.forename: Arnab
authors.initials: A
authors.lastname: Nayek
authors.affiliation: Authors equally contributed.
authors.forename: Shyamashree
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104.
authors.forename: Pratyay
authors.initials: P
authors.lastname: Seth
authors.affiliation: Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104.
authors.forename: Sunit
authors.initials: S
authors.lastname: Das
authors.affiliation: Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104.
authors.forename: Vishma Pratap
authors.initials: VP
authors.lastname: Sur
authors.affiliation: Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104.
authors.forename: Chittran
authors.initials: C
authors.lastname: Roy
authors.affiliation: Department of Biotechnology, The University of Burdwan, Golapbag, Burdwan, 713104.
authors.forename: Amal Kumar
authors.initials: AK
authors.lastname: Bandyopadhyay
keywords: bond multiplicity; core; intra helical; isolated; networked; salt-bridge; surface