Detection of long-range concerted motions in protein by a distance covariance
Open accessAbstract
We asses the ability of a distance correlation coefficient (DiCC), calculated from distance covariance, for detecting long-range concerted motion in proteins. We establish a set of criteria for ideal correlation coefficient values based on the coefficient of determination in multidimension, R 2 . We compare in detail DiCC and conventional correlation coefficients against these criteria. We demonstrate that, in contrast to conventional correlation coefficients, which capture long-distance correlation adequately only with certain restrictions in multidimension, DiCC reflects appropriate correlation in both one-dimension and multidimensions. Finally, we demonstrate the usefulness of DiCC for assessing long-distance correlated fluctuation in protein dynamics.
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Distance correlation has theoretical advantages over Pearson's coefficient and has been recently used in biological applications.
“A more sophisticated measure of association between variables is the distance correlation method [57,58], which has theoretical advantages over Pearson's coefficient and has been recently used in biological applications [59,60].”
From Reverse engineering and identification in systems biology: strategies, perspectives and challenges (2014) · cites this paper as [59]
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Self-citation
- Authors
- Roy, A., & Post, C. B.
- Affiliations
- Purdue University West Lafayette (US)
- Corresponding author
- Roy, Amitava
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-08-30
- Volume
- 8
- Issue
- 9
- Pages
- 3009-3014
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- PMC
- PMC3630994
- OpenAlex
- W2319880230
- Cited by
- 21
- References
- 20
- Citations by year
- 2025: 1 · 2024: 3 · 2023: 1 · 2021: 1 · 2020: 4 · 2019: 1 · 2018: 2 · 2015: 3 · 2014: 2 · 2013: 3
- FWCI
- 1.03
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Chemical Theory and Computation (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Purdue University
- National Institutes of Health
- National Institute of Allergy and Infectious Diseases (R01AI039639)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Social Sciences › Economics, Econometrics and Finance › Economics and Econometrics › Complex Systems and Time Series Analysis
- Keywords
- distance covariance, protein dynamics, protein fluctuations, correlation coefficient, R-squared
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