The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Relation between Free Energy Landscapes of Proteins and Dynamics
Open accessAbstract
By examining the molecular dynamics (MD) of protein folding trajectories, generated with the coarse-grained UNRES force field, for the B-domain of staphylococcal protein A and the triple β-strand WW domain from the Formin binding protein 28 (FBP), by principal component analysis (PCA), it is demonstrated how different free energy landscapes (FELs) and folding pathways of trajectories can be, even though they appear to be very similar by visual inspection of the time-dependence of the root-mean-square deviation (rmsd). Approaches to determine the minimal dimensionality of FELs for a correct description of protein folding dynamics are discussed. The correlation between the amplitude of the fluctuations of proteins and the dimensionality of the FELs is shown. The advantage of internal coordinate PCA over Cartesian PCA for small proteins is also illustrated.
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Principal Component Analysis for Protein Folding Dynamics
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Self-citationTransition networks for modeling the kinetics of conformational change in macromolecules
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Cited by
Revealing Free Energy Landscape From MD Data via Conditional Angle Partition Tree
Jiang, H., Li, H., Wong, W. H., & Fan, X. (2023) · IEEE/ACM Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2022.3172352 · Cited by 4
Metadata
- Authors
- Maisuradze, G. G., Liwo, A., & Scheraga, H. A.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2010-01-13
- Volume
- 6
- Issue
- 2
- Pages
- 583-595
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2104806389
- Cited by
- 264
- References
- 48
- FWCI
- 2.48
- Type
- journal article
- Language
- en
- Open access
- green
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