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Download fileUsing Tensor Analysis to characterize Contact-map Dynamics of Proteins
journal contribution
posted on 2004-04-01, 00:00 authored by Arvind Ramanathan, Pratul K. Agarwal, Christopher J. LangmeadMolecular dynamics simulations provide vast amount of information about a protein’s dynamics.
To interpret a protein’s dynamics and how it may relate to its function, traditionally, two-way
analysis techniques such as principal component analysis have been used. However, two-way
analysis techniques are usually limited by the fact that they have to be done post-process, i.e.,
after the simulations have been run and also cannot provide insights into temporal behavior of a
protein. To overcome these limitations, we are proposing to use multi-way analysis techniques to
understand and interpret protein dynamics as and when the simulations are progressing i.e., online.
We model MD simulations in terms of a collection of contact maps and then modeling them as
tensors to capture multiple dependencies. Using two recently developed techniques to perform
online analysis of streaming data, we illustrate the use of this technique to describe and interpret
the behavior of a protein complex in real time. We provide both experimental evidence to support
our claims and also discuss the potential advantages and disadvantages of using tensor analysis
techniques.