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Entropy 2012, 14(2), 213-232; doi:10.3390/e14020213

Article

Quantitative Comparison of Conformational Ensembles

Kevin C. Wolfe and Gregory S. Chirikjian*

Department of Mechanical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA

* Author to whom correspondence should be addressed.

Received: 1 January 2012; in revised form: 27 January 2012 / Accepted: 3 February 2012 / Published: 10 February 2012

(This article belongs to the Special Issue Loop Entropy)

Download PDF Full-Text [878 KB, uploaded 10 February 2012 09:58 CET]

Abstract: A number of measures have been used in the structural biology literature to compare the shapes or conformations of biological macromolecules. However, the issue of how to compare two ensembles of conformations has received far less attention. Herein, the problem of how to quantitatively compare two such ensembles is addressed in several different ways using concepts from probability and information theory. Ultimately, such metrics could be used in the evaluation of structure-prediction algorithms and the analysis of how conformational mobility is inhibited by bound ligands.

Keywords: loop entropy; Kullback-Leibler divergence; Gaussian distributions; elastic networks

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