ADSBET2: AUTOMATED DETERMINATION OF SALT BRIDGE ENERGY TERMS, version 2.0
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Feature:
a. SBS Energy-terms in general [kcal/mol] and normalized [kcal/mol/bond] format
Only the LATER is comparable among SBSs and hence help for their statictical analyses
b. Combines energy terms in NSBS and ISBS format
NSBS-> Networked SBS forms - 1:2 [dimer], 1:3 [trimer] etc;
NSBS types-> ie base-networked SBS and acid networked SBS
ISBS- Isolated SBS form - 1:1 form[monomer]
g. Accessible surface area ie ASA in NSBS and ISBS form;
the program uses SURFACE-RACER [option 4] /POPS [option 5] /NACCESS option 6]
h. ddGprot [hence ddGnet] in two categories based on source of charges
ddGprot-I: partial charges due to all-sides [Nayek et al, 2014]
ddGprot-II: Partial charges due to acidic and basic residues [Kumar and Nussinov, 1999]
k. two models for interacting side-chains:
Model-1: As in ADSBET [Nayek et al, 2015 ]
Model-2: A New additional model [the most popular and well adapted one]
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Author:
Nayek A, Sen Gupta PS, Banerjee S, Sur VP, Das S, Seth, P, Islam RNU and Bandyopadhyay AK*;
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Citation:
APBS Adaptive Poisson-Boltzmann Solver; Version 1.4.1
1] Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems:
application to microtubules and the ribosome. PNAS USA 98, 10037-10041 2001.
PDB2PQR
2] Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. PDB2PQR: an automated pipeline for
the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 2004
SBION:
3] A Program for Analyses of Salt-Bridges from Multiple Structure Files,
Parth Sarthi Sen Gupta, Sudipta Mondal, Buddhadev Mondal, Rifat Nawaz Ul Islam,
Shyamashree Banerjee & Amal K Bandyopadhyay
Bioinformation 10 03: 164-166 2014
SBION2:
4] Analyses of Salt Bridges from Multiple Structure Files, Version 2
Parth Sarthi Sen Gupta, Arnab Nayek, Shyamashree Banerjee1, Pratyay Seth,
Sunit Das, Vishma Pratap Sur, & Amal K Bandyopadhyay
Bioinformation 11 01: 39-42 2015
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INSTALLATION
1. download ADSBET2, from source-forge and unzip in a folder where RCSB-PDB files are present
2. open cygwin (32 bit) B-SHELL or C-SHELL prompt
3. type ./ADSBET2.exe [enter] and follow instruction there
NOTE: The program is supplied with one pdb file i.e. 1DOI.pdb
thus user can immediately run the program with the supplied file
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Other-programs to be installed in mentioned directory for functioning of the program
apbs.exe - download from [ http://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.0/ ] and
install in "./afp/apbs" dir
pdb2pqr - download from [ http://sourceforge.net/projects/pdb2pqr/files/pdb2pqr/pdb2pqr-1.9.0/ ] and
install in "./afp/pqr" dir
NACCESS - for ASA by naccess method, instruction in web-page: [http://www.bioinf.manchester.ac.uk/naccess/]
working instruction in mentioned in README-NACCESS (present in ./afp/naccess)
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For any query/difficulty/suggestion-for-improvement please contact:
akbanrjee@biotech.buruniv.ac.in
