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Diversity and motif conservation in protein 3D structural landscape: exploration by a new multivariate simulation method

  • Rajani R. Joshi
Original Paper
  • 59 Downloads

Abstract

In this paper, diversity and conservation in the ‘landscape’ of random variation of protein tertiary structures are explored for quantitative feature-vector models of major types of functionally important 3D structural motifs. For this, I have deployed a recently developed nonparametric regression (NPR)-based multidimensional copula method of simulation. Apart from improved accuracy of multidimensional random sample generation, the simulation provides additional insight into diversity in the protein structural landscape in terms of random variation in the feature-vector. It shows the relative importance of several features, with biological implications, in conservation of motifs. Mapping of this landscape in distance-preserving 2D eigenspace also shows consistency in demarcation of different motif classes and preservation of their characteristic patterns in this 2D space.

Keywords

Protein tertiary structural motifs Multi-dimensional feature vector Random number generation Copulas Nonparametric regression Multidimensional scaling 

Notes

Acknowledgements

The author would like to thank Srijit Chakrabarty for implementing the initial version of the author’s algorithm as part of his MSc project. The version used in this work has been developed further with significant modifications.

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of MathematicsIndian Institute of Technology BombayMumbaiIndia

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