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ADSBET2: Automated Determination of Salt-Bridge Energy-Terms version 2

Component (bridge: ΔΔG(brd), background: ΔΔG(prot), desolvation: ΔΔG(dsolv)) and net (ΔΔG(net)) energy-terms of salt-bridge-structure (SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS) method. While the procedure reports gross ene...

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Detalles Bibliográficos
Autores principales: Nayek, Arnab, Gupta, Parth Sarthi Sen, Banerjee, Shyamashree, Sur, Vishma Pratap, Seth, Pratyay, Das, Sunit, Islam, Rifat Nawaz Ul, Bandyopadhyay, Amal Kumar
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574125/
https://www.ncbi.nlm.nih.gov/pubmed/26420923
http://dx.doi.org/10.6026/97320630011413
Descripción
Sumario:Component (bridge: ΔΔG(brd), background: ΔΔG(prot), desolvation: ΔΔG(dsolv)) and net (ΔΔG(net)) energy-terms of salt-bridge-structure (SBS) are auto-generated by the program ADSBET that makes use of general purpose Adaptive Poison Boltzmann Solver (APBS) method. While the procedure reports gross energy terms (Kcal Mol(-1)), report on bond-multiplicity corrected normalized energyterms (Kcal Mol(-1) Bond(-1)) along with their accessibility (ASA) in monomer, isolated-SBS (ISBS) and networked-SBS (NSBS) format would be very useful for statistical comparison among SBSs and understanding their location in protein structure. In this end, ADSBET2 potentially incorporates these features along with additional model for side-chain. Gross and normalized energy-terms are redirected in monomer, ISBS and NSBS format along with their ASA informations. It works on any number of SBSs for any number of structure files present in a database. Taken together, ADSBET2 has been suitable for statistical analyses of SBSs energetics and finds applications in protein engineering and structural bioinformatics. AVAILABILITY: ADSBET2 is freely available at http://sourceforge.net/projects/ADSBET2/ for all users.