Preprint Review Version 1 Preserved in Portico This version is not peer-reviewed

Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules

Version 1 : Received: 11 May 2022 / Approved: 12 May 2022 / Online: 12 May 2022 (10:53:37 CEST)

A peer-reviewed article of this Preprint also exists.

Kitao, A. Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules. J 2022, 5, 298-317. Kitao, A. Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules. J 2022, 5, 298-317.

Journal reference: J 2022, 5, 21
DOI: 10.3390/j5020021

Abstract

Principal component analysis (PCA) is used to reduce the dimensionalities of high dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods, and their applications for investigating protein dynamics.

Keywords

principal component analysis; collective variables; molecular dynamics; energy landscape; solvent effects; linear response theory; independent component analysis

Subject

LIFE SCIENCES, Biophysics

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