Format

Send to

Choose Destination
Methods Mol Biol. 2014;1084:193-226. doi: 10.1007/978-1-62703-658-0_11.

Principal component analysis: a method for determining the essential dynamics of proteins.

Author information

1
Department of Physics and Optical Science, University of North Carolina, Charlotte, NC, USA.

Abstract

It has become commonplace to employ principal component analysis to reveal the most important motions in proteins. This method is more commonly known by its acronym, PCA. While most popular molecular dynamics packages inevitably provide PCA tools to analyze protein trajectories, researchers often make inferences of their results without having insight into how to make interpretations, and they are often unaware of limitations and generalizations of such analysis. Here we review best practices for applying standard PCA, describe useful variants, discuss why one may wish to make comparison studies, and describe a set of metrics that make comparisons possible. In practice, one will be forced to make inferences about the essential dynamics of a protein without having the desired amount of samples. Therefore, considerable time is spent on describing how to judge the significance of results, highlighting pitfalls. The topic of PCA is reviewed from the perspective of many practical considerations, and useful recipes are provided.

PMID:
24061923
PMCID:
PMC4676806
DOI:
10.1007/978-1-62703-658-0_11
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Springer Icon for PubMed Central
Loading ...
Support Center