Please use this identifier to cite or link to this item: doi:10.22028/D291-30504
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Title: Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes
Author(s): Ahmad, Mazen
Helms, Volkhard
Kalinina, Olga V.
Lengauer, Thomas
Language: English
Title: Journal of chemical theory and computation : JCTC
Volume: 15
Issue: 4
Startpage: 2166
Endpage: 2178
Publisher/Platform: ACS
Year of Publication: 2019
Publikation type: Journal Article
Abstract: A new method termed "Relative Principal Components Analysis" (RPCA) is introduced that extracts optimal relevant principal components to describe the change between two data samples representing two macroscopic states. The method is widely applicable in data-driven science. Calculating the components is based on a physical framework that introduces the objective function (the Kullback-Leibler divergence) appropriate for quantifying the change of the macroscopic state affected by the changes in the microscopic features. To demonstrate the applicability of RPCA, we analyze the thermodynamically relevant conformational changes of the protein HIV-1 protease upon binding to different drug molecules. In this case, the RPCA method provides a sound thermodynamic foundation for analyzing the binding process and thus characterizing both the collective and the locally relevant conformational changes. Moreover, the relevant collective conformational changes can be reconstructed from the informative latent variables to exhibit both the enhanced and the restricted conformational fluctuations upon ligand association.
DOI of the first publication: 10.1021/acs.jctc.8b01074
URL of the first publication:
Link to this record: hdl:20.500.11880/28884
ISSN: 1549-9626
Date of registration: 20-Mar-2020
Faculty: NT - Naturwissenschaftlich- Technische Fakultät
Department: NT - Biowissenschaften
Professorship: NT - Prof. Dr. Volkhard Helms
Collections:SciDok - Der Wissenschaftsserver der Universität des Saarlandes

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