Elucidating protein

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.The nucleocapsid (N) protein of Chandipura virus (CHPV) plays a crucial role in viral life cycle, besides being an important structural component of the virion through proper organization of its interactions with other viral proteins.In many cases, we utilize knowledge-based potentials deduced from large data sets like multiple sequence alignments or protein structures to corroborate characteristic properties of proteins or residue-positions.Thus, we deduce properties that can contribute to a classification by means of support vector machines or other state-of-the-art classifiers.

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The ~11 kb genome of CHPV [5] is encapsidated by nucleocapsid (N) protein and serves as a template for both replication and transcription.

Using these methods, we can plan wet-lab experiments together with our collaboration partners.

We are also interested in elucidating protein evolution by means of phylogenetic methods.

In this direction, we have generated the structure of CHPV N protein by homology modeling using SWISS-MODEL workspace and Accelrys Discovery Studio client 2.55 and mapped the domains of N protein using Pi SQRD.

The interactions of N protein fragments with other proteins were determined by ZDOCK rigid-body docking method and validated by yeast two-hybrid and ELISA.

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