SBION2 Files

README
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Program: SBION2 for Analysis of Salt Bridges on X-ray Structure
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

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INSTRUCTION: 

THE PROGRAM IS EXTENSIVELY TESTED TO FUNCTION ON CYGWIN WITH both C-SHELL/B_SHELL

1. Download SBION2 ("sbion2.zip") from its home page -- << sourceforge.net >>
2. unzip the content - README (this file) and "WORK"-directory will be visible with two sample pdb files (1ITK.pdb,1GAQ.pdb) 
3. 'cd' to "WORK" directory.


3. In SHELL prompt type ./sbion2.exe h and follow up instruction there

The program run in three different modes with three different arguments [1 OR 2 OR 3]
option 1 -- program use SURFACE RACER -Tsodikov et al 2002 for accessibility for Core-surf location of salt-bridges
option 2 -- program use NACCESS - Hubbard and Thronton, 1993 for accessibility for Core-surf location of salt-bridges
option 3 -- program run analyze salt-bridges without core-surface categorization

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SBION2 Vs SBION (Gupta et al Bioinformation, 10, 164-166, 2014) :
SBION2 contains many improvements (see below) over the earlier one (SBION).comprehensive analysis of 
salt bridges, user friendly outputs has been its major attribute.
 
FEATURES:
common		a] structures			any number with .pdb extension 
common		b] chains		 	all chains in structures
common		c] sb distance			user choice
NEW		d] Local threshold		user choice
NEW		e] core threshold		user choice
common		f] ugly PDBs			corrected
common		g] NMR files			screened out
common		h] missing res			reported
NEW		i] sb distance			averaged over sb partners interactions
NEW		j] Binary outputs		in excel format
Improved	k] res distribution		acidic (D, E) and basic (K, H, R):
				in prot: 	in sec struct (ie sht, hlx, coil- in core & surf);
				in sb:   	in sec struct (ie sht, hlx, coil- in core & surf);
NEW		l] intervene res dist		three outputs- wrt all, isolated and networked pairs
NEW		m] supplimentary table		for direct use in publication purpose
NEW		n] versatile ASA calc	 	either SURFACE RACER or NACCESS
NEW		o] General output	 	MISSING res, NETWORKED sb and protein-protein interaction

NEW		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


NEW		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

Input: 		PDB file in .pdb format (available at RCSB)
Interpretor:    AWK - Aho AV, Kernighan BW, Weinberger PJ 1977
Bug report:	akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;
    
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OUTPUTs:
    
1  a_FREQUENCY_ISOLATED_SB_co_su 				a_FREQUENCY_NETWORKED_SB_co_su
2  b_iso_SINGLE_bond_MULTIPLICITY_co_su				b_net_SINGLE_bond_MULTIPLICITY_co_su
3  c_iso_MULTIPLE_bond_MULTIPLICITY_SUM_co_su	 		c_net_MULTIPLE_bond_MULTIPLICITY_SUM_co_su
4  d_iso_MULTIPLE_bond_MULTIPLICITY_FREQ_co_su			d_net_MULTIPLE_bond_MULTIPLICITY_FREQ_co_su
5  e_iso_HYDROGEN_BONDED_SB_FREQ_co_su				e_net_HYDROGEN_BONDED_SB_FREQ_co_su
6  f_iso_nonHYDROGEN_BONDED_SB_FREQ_co_su			f_net_nonHYDROGEN_BONDED_SB_FREQ_co_su	
7  g_iso_SEC_STRUCT_and_SB_PAIR_sp_FREQ				g_net_SEC_STRUCT_and_SB_PAIR_sp_FREQ
8  h_iso_LOCAL_SALT_BRIDGE					h_net_LOCAL_SALT_BRIDGE
9  i_iso_nonLOCAL_SALT_BRIDGE					i_iso_nonLOCAL_SALT_BRIDGE
10 j_iso_CORE_INTRA_INTER_HLX_SHT_COIL_interaction		j_net_CORE_INTRA_INTER_HLX_SHT_COIL_interaction	
11 j_iso_SURF_INTRA_INTER_HLX_SHT_COIL_interaction		j_net_SURF_INTRA_INTER_HLX_SHT_COIL_interaction


12 Protein_ACIDIC_res_DISTRIBUTION_in_P_SB_ss_co_su	
13 Protein_BASIC_res_DISTRIBUTION_in_P_SB_ss_co_su

14 Protein_Isolated_Pair_intervenning_table
15 Protein_Networked_Pair_intervenning_table
16 SB_total_intervenning

17 Supplimentary_Table
18 General
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*note- Surface_core clasess are absent for runing the program SBION2 with argument 3
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Description of outputs:

Program redirects 11 pairs (file 1 - 11; Table 1) EXCEL files for itemized BINARY COMPARISON of salt bridges.
Files 12 & 13 are for distribuition of acidic and basic residue in protein, in salt bridge, in secondary structure.
files 14 - 16 are intervening residue tables for isolated, networked and total salt bridges.
file 17 is the supplementary table that present comprehensive list of detail for only one unique chain 
(should be good for publication purpose).
File 18 describes details of missing residue, P-P interaction & network salt bridges.

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WHAT PLATFORMS ARE SUPPORTED?

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SBION2 is designed to operate under a flavour of Unix/or unix like environment (CYGWIN)  

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FEEDBACK

Encouragement, bug reports (patches are welcome), suggestions and 
constructive criticism 
may be sent to akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;. I don't 
always have time to read my mail or to reply promptly, 
but I will do my best.


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Appendix table 1 -  Files supplied as part of SBION2

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Directories	no. of files		name of files					comments
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WORK		 4			SBION2.exe(APPLICATION),radii.txt,		it also contains 1 dir "apf"
					1GAQ.pdb and 1 ITK.pdb
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apf		 13			"abc";"casts"; "coca"; "coka"; 			it contains 3 dirs "app",
                      			"colsb";"gsbpdb";"mssd";"pdbdes";		"naccess","exedir" & "Surface_racer"
					"sbanalr";"sbnall";"stwob","tsod",
				 	 pdbfile.exe".
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exedir		 2			"grunns.exe","grunts.exe",				none

app		 10			"abd; btwos; castc; despdb; dssm; nalsb;	it contains 1 dir "exedir"
					 pdbgsb; ranalsb; sbcol" & 
					 pdbfilef.exe"

exedir		 1		 	"grunza.exe"						none

naccess**	 4		 	accall.exe, standard.data, vdw.radii &	none
					readme.txt

Surface_racer**	 3		 	tsodikov.exe, radii.txt & readme.txt		 	none
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**-mentioned file could	be installed in the define directory as per instruction mentioned in readme file 
(surface racer_readme & naccess_readme) present in the respective directories.	


END of README