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Papers by Balaji Kale
Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics
Journal of Biomolecular Structure & Dynamics, 2012
The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecul... more The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecular dynamics (MD) simulation using all-atom model. Based on the trajectory analysis, three prominent conformational models were proposed for GT1B. Direct and water-mediated hydrogen bonding interactions stabilize these structures. The molecular modeling and 15 ns MD simulation of the Botulinum Neuro Toxin/B (BoNT/B) – GT1B complex revealed that BoNT/B can accommodate the GT1B in the single binding mode. Least mobility was seen for oligo-GT1B in the binding pocket. The bound conformation of GT1B obtained from the MD simulation of the BoNT/B-GT1B complex bear a close conformational similarity with the crystal structure of BoNT/A-GT1B complex. The mobility noticed for Arg 1268 in the dynamics was accounted for its favorable interaction with terminal NeuNAc. The internal NeuNAc1 tends to form 10 hydrogen bonds with BoNT/B, hence specifying this particular site as a crucial space for the therapeutic design that can restrict the pathogenic activity of BoNT/B.
Journal of Information Technology, 2009
The mobile ecosystem is characterized by a large and complex network of companies interacting wit... more The mobile ecosystem is characterized by a large and complex network of companies interacting with each other, directly and indirectly, to provide a broad array of mobile products and services to end-customers. With the convergence of enabling technologies, the complexity of the mobile ecosystem is increasing multifold as new actors are emerging, new relations are formed, and the traditional distribution of power is shifted. Drawing on theories of network science, complex systems, interfirm relationships, and the creative art and science of visualization, this paper identifies key players and maps the complex structure and dynamics of nearly 7000 global companies and over 18,000 relationships in the converging mobile ecosystem. Our approach enables decision makers to (i) visually explore the complexity of interfirm relations in the mobile ecosystem, (ii) discover the relation between current and emerging segments, (iii) determine the impact of convergence on ecosystem structure, (iv) understand a firm's competitive position, and (v) identify interfirm relation patterns that may influence their choice of innovation strategy or business models.
Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics
Journal of Biomolecular Structure & Dynamics, 2012
The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecul... more The conformational property of oligosaccharide GT1B in aqueous environment was studied by molecular dynamics (MD) simulation using all-atom model. Based on the trajectory analysis, three prominent conformational models were proposed for GT1B. Direct and water-mediated hydrogen bonding interactions stabilize these structures. The molecular modeling and 15 ns MD simulation of the Botulinum Neuro Toxin/B (BoNT/B) – GT1B complex revealed that BoNT/B can accommodate the GT1B in the single binding mode. Least mobility was seen for oligo-GT1B in the binding pocket. The bound conformation of GT1B obtained from the MD simulation of the BoNT/B-GT1B complex bear a close conformational similarity with the crystal structure of BoNT/A-GT1B complex. The mobility noticed for Arg 1268 in the dynamics was accounted for its favorable interaction with terminal NeuNAc. The internal NeuNAc1 tends to form 10 hydrogen bonds with BoNT/B, hence specifying this particular site as a crucial space for the therapeutic design that can restrict the pathogenic activity of BoNT/B.
Journal of Information Technology, 2009
The mobile ecosystem is characterized by a large and complex network of companies interacting wit... more The mobile ecosystem is characterized by a large and complex network of companies interacting with each other, directly and indirectly, to provide a broad array of mobile products and services to end-customers. With the convergence of enabling technologies, the complexity of the mobile ecosystem is increasing multifold as new actors are emerging, new relations are formed, and the traditional distribution of power is shifted. Drawing on theories of network science, complex systems, interfirm relationships, and the creative art and science of visualization, this paper identifies key players and maps the complex structure and dynamics of nearly 7000 global companies and over 18,000 relationships in the converging mobile ecosystem. Our approach enables decision makers to (i) visually explore the complexity of interfirm relations in the mobile ecosystem, (ii) discover the relation between current and emerging segments, (iii) determine the impact of convergence on ecosystem structure, (iv) understand a firm's competitive position, and (v) identify interfirm relation patterns that may influence their choice of innovation strategy or business models.