SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files
| Autor: | Amal Kumar Bandyopadhyay, Buddhadev Mondal, Rifat Nawaz Ul Islam, Sudipta Mondal, Shyamashree Banerjee, Parth Sarthi Sen Gupta |
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| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Structure (mathematical logic)
Protein structure database salt-bridges Process (engineering) Computer science business.industry Distributed computing Stability (learning theory) Context (language use) network salt bridges General Medicine stability computer.software_genre proteins Software Protein folding Data mining program business computer Protein secondary structure |
| Zdroj: | Bioinformation |
| ISSN: | 0973-2063 0973-8894 |
| Popis: | Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges. While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION which can perform all the above mentioned computations for any number of protein with any number of chain at any given distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses potential for applications in the field of structural and comparative bioinformatics studies. Availability SBION is freely available for non-commercial/academic institutions on formal request to the corresponding author (ni.ca.vinurub.hcetoib@eejrenabka). |
| Databáze: | OpenAIRE |
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