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ADSBET2: AUTOMATED DETERMINATION OF SALT BRIDGE ENERGY TERMS, version 2.0
Author:c)--Arnab Nayek, Parth Sarthi Sen Gupta, Shyamashree Banerjee,Vishma Pratap Sur, Pratay Seth, Sunit Das, Rifat Nawaz Ul Islam and Amal K bandyopadhyay*
Department of Biotechnology,The University of Burdwan, India
Features
- 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.
- 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]
- Accessible surface area ie ASA in NSBS and ISBS form; the program uses SURFACE-RACER [option 4] /POPS [option 5] /NACCESS option 6]
- 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]
- 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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