SBION2

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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