Issue 37, 2022

Information-theoretical measures identify accurate low-resolution representations of protein configurational space

Abstract

The steadily growing computational power employed to perform molecular dynamics simulations of biological macromolecules represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data are produced, from which useful, synthetic, and intelligible information has to be extracted to make the crucial step from knowing to understanding. Here we tackled the problem of coarsening the conformational space sampled by proteins in the course of molecular dynamics simulations. We applied different schemes to cluster the frames of a dataset of protein simulations; we then employed an information-theoretical framework, based on the notion of resolution and relevance, to gauge how well the various clustering methods accomplish this simplification of the configurational space. Our approach allowed us to identify the level of resolution that optimally balances simplicity and informativeness; furthermore, we found that the most physically accurate clustering procedures are those that induce an ultrametric structure of the low-resolution space, consistently with the hypothesis that the protein conformational landscape has a self-similar organisation. The proposed strategy is general and its applicability extends beyond that of computational biophysics, making it a valuable tool to extract useful information from large datasets.

Graphical abstract: Information-theoretical measures identify accurate low-resolution representations of protein configurational space

Supplementary files

Article information

Article type
Paper
Submitted
16 5月 2022
Accepted
26 7月 2022
First published
07 9月 2022
This article is Open Access
Creative Commons BY-NC license

Soft Matter, 2022,18, 7064-7074

Information-theoretical measures identify accurate low-resolution representations of protein configurational space

M. Mele, R. Covino and R. Potestio, Soft Matter, 2022, 18, 7064 DOI: 10.1039/D2SM00636G

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