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3D Perception of Maximum Density Zone on Ramachandran Plots for Zika Virus Protein Structures

Mayukh Mukhopadhyay, Parama Bhaumik
doi: https://doi.org/10.1101/053074
Mayukh Mukhopadhyay
1Tata Consultancy Services, Kolkata-700091
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Parama Bhaumik
2Department of Information Technology, Jadavpur University, Kolkata-700098
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Abstract

The Ramachandran plot is among the most central concepts in structural biology which uses torsion angles to describe polypeptide and protein conformation. To help visualize the features of high-fidelity Ramachandran plots, it is helpful to look beyond the common two-dimensional psi-phi-plot, which for a large dataset does not serve very well to convey the true nature of the distribution. In particular, when a large subset of the observations is found very narrowly distributed within one small region, this is not well seen in the simple plot because the data points congest one another. Zika Virus (ZIKV) protein databank has been chosen as specimen for analysis. This is because the structure, tropism, and pathogenesis of ZIKV are largely unknown and are the focus of current investigations in an effort to address the need for rapid development of vaccines and therapeutics. After a brief survey on Zika Virus, it is shown that when a dense dataset of ZIKV protein databank is passed through a colour-coded scaled algorithm, a three dimensional plot gets generated which gives a much more compelling impression of the proportions of residues in the different parts of the protein rather than representing it in a normal two dimensional psi-phi plot.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 12, 2016.
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3D Perception of Maximum Density Zone on Ramachandran Plots for Zika Virus Protein Structures
Mayukh Mukhopadhyay, Parama Bhaumik
bioRxiv 053074; doi: https://doi.org/10.1101/053074
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3D Perception of Maximum Density Zone on Ramachandran Plots for Zika Virus Protein Structures
Mayukh Mukhopadhyay, Parama Bhaumik
bioRxiv 053074; doi: https://doi.org/10.1101/053074

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