SBION2

Program: SBION2- Analyses of Salt Bridges from Multiple Structure Files,
Version:--v2.0 - improved version of SBION: Gupta et al Bioinformation, 10, 164-166, 2014
Author:c)--Parth Sarthi Sen Gupta, Arnab Nayek, Shyamashree Banerjee, Pratyay Seth, Vishma Pratap Sur, Sunit Das,Chittran Roy and Amal Kumar Bandyopadhyay;
Department of Biotechnology,The University of Burdwan, India

Features

a] SBION2 can process any number of structures with .pdb extension
b] chains ----- all chains in structures
c] salt bridge(sb) distance ----- user choice
d] Local threshold ----- user choice
e] core threshold ----- user choice
f] ugly PDBs ----- corrected
g] NMR files ----- screened out
h] missing residue ----- reported
i] sb distance ----- averaged over sb partners interactions
j] Binary outputs ----- in excel format
k] res distribution ----- acidic (D, E) and basic (K, H, R): ; in protein: in sec struct (ie sht, hlx, coil- in core & surf); in sb: in sec struct (ie sht, hlx, coil- in core & surf);
l] intervening residue distance ----- three outputs- w.r.t all, isolated and networked pairs
m] supplimentary table ----- for direct use in publication purpose
n] versatile ASA calc ----- either SURFACE RACER or NACCESS
o] General output ----- MISSING res, NETWORKED sb and protein-protein interaction
p] BINARY ANALYSIS: KD, KE, HD, HE, RD and RE specific ----- ISOLATED vs NETWORKED SB in CORE vs SB in SURFACE; HYDROGEN BONDED vs NON-HYDROGEN BONDED; LOCAL SB vs NON-LOCAL SB; SINGLE BOND vs MULTIPLE BOND; SEC STRUCT vs COIL; INTRA-HELICAL vs INTER-HELICAL; INTRA-STRAND vs INTER-STRAND.
q] ORIENTATION PREFERENCE ANALYSIS: KD, KE, HD, HE, RD and RE specific ----- D,E for NT or CT in INTRA-HELICAL or INTRA-STRAND interaction; D,E in COIL for RIGHT or LEFT of HELIX in local HELIX-COIL interaction; D,E in COIL for RIGHT or LEFT of STRAND in local STRAND-COIL interaction; K,H,R in COIL for RIGHT or LEFT of HELIX in local HELIX-COIL interaction; K,H,R in COIL for RIGHT or LEFT of STRAND in local STRAND-COIL interaction.

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