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.

Project Samples

Project Activity

See All Activity >

Follow SBION2

SBION2 Web Site

Other Useful Business Software

Our Free Plans just got better! | Auth0

With up to 25k MAUs and unlimited Okta connections, our Free Plan lets you focus on what you do best—building great apps.

You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.

Try free now

Rate This Project