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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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