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Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins
Open accessAbstract
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.
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Huber, P. J. (1981) · Wiley Series in Probability and Statistics · doi:10.1002/0471725250 · Cited by 7,066
Sparse Principal Component Analysis
Zou, H., Hastie, T., & Tibshirani, R. (2006) · Journal of Computational and Graphical Statistics · doi:10.1198/106186006x113430 · Cited by 3,152
Cited by
Singh, A. K., Kushwaha, P. P., Prajapati, K. S., Shuaib, M., Gupta, S., & Kumar, S. (2021) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2020.104185 · Cited by 58
Effective Molecular Dynamics from Neural Network-Based Structure Prediction Models
Jussupow, A., & Kaila, V. R. I. (2023) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.2c01027 · Cited by 42
Tang, Z., Chen, S.-H., & Chang, C.-E. A. (2020) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.9b01153 · Cited by 28
Wang, R.-R., Liu, W.-S., Zhou, L., Ma, Y., & Wang, R.-L. (2020) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2019.1613266 · Cited by 21
Metadata
- Authors
- David, C. C., & Jacobs, D. J.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2013-09-03
- Volume
- 1084
- Pages
- 193-226
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2292301738
- Cited by
- 1,252
- References
- 2
- FWCI
- 16.58
- Type
- book chapter
- Language
- en
- Open access
- green
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- David, C. C., & Jacobs, D. J. (2014). Principal Component Analysis: A Method for Determining the Essential Dynamics of Proteins. Methods in Molecular Biology. https://doi.org/10.1007/978-1-62703-658-0_11
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