The DOI matches its Crossref record; 132 of the 133 references it cites were found in a registry or an index.
Protein Folding Theory: From Lattice to All-Atom Models
Abstract
▪ Abstract This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.
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“AlphaFold does not resolve the decades-long protein folding challenge, nor does it identify the folding pathways.”
From AlphaFold, Artificial Intelligence (AI), and Allostery (2022) · cites this paper as [56]
Citations
Cites
From Levinthal to pathways to funnels
Dill, K. A., & Chan, H. S. (1997) · Nature Structural & Molecular Biology · doi:10.1038/nsb0197-10 · Cited by 2,293
Structure and Mechanism in Protein Science
Fersht, A. (2017) · WORLD SCIENTIFIC eBooks · doi:10.1142/10574 · Cited by 2,053
Structure and Mechanism in Protein Science. A guide to Enzyme Catalysis and Protein Folding
Howland, J. L. (2001) · Biochemistry and Molecular Biology Education · Cited by 1,823
Spin glasses and the statistical mechanics of protein folding.
Bryngelson, J. D., & Wolynes, P. G. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.21.7524 · Cited by 1,647
Plaxco, K. W., Simons, K. T., & Baker, D. A. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1645 · Cited by 1,515
Duan, Y., & Kollman, P. A. (1998) · Science · doi:10.1126/science.282.5389.740 · Cited by 1,337
Theory for the folding and stability of globular proteins
Dill, K. A. (1985) · Biochemistry · doi:10.1021/bi00327a032 · Cited by 1,256
Clementi, C., Nymeyer, H., & Onuchic, J. N. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3693 · Cited by 1,228
Šali, A., Shakhnovich, E. I., & Karplus, M. (1994) · Nature · doi:10.1038/369248a0 · Cited by 951
Self-citationProtein folding funnels: a kinetic approach to the sequence-structure relationship.
Leopold, P., Montal, M., & Onuchic, J. N. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.18.8721 · Cited by 929
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Dill, K. A., Ozkan, S. B., Shell, M. S., & Weikl, T. R. (2008) · Annual Review of Biophysics · doi:10.1146/annurev.biophys.37.092707.153558 · Cited by 1,163
Coarse-Grained Protein Models and Their Applications
Kmiecik, S., Gront, D., Koliński, M., Wieteska, Ł., Badaczewska-Dawid, A. E., & Koliński, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00163 · Cited by 1,113
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 907
Levine, R. D. (2005) · Cambridge University Press eBooks · doi:10.1017/cbo9780511614125 · Cited by 863
The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology
Fogolari, F., Brigo, A., & Molinari, H. (2002) · Journal of Molecular Recognition · doi:10.1002/jmr.577 · Cited by 587
Metadata
- Authors
- Mirny, L., & Shakhnovich, E.
- Affiliations
- Harvard University (US)
- Venue
- Annual Review of Biophysics and Biomolecular Structure
- Publisher
- Annual Reviews
- Published
- 2001-06
- Volume
- 30
- Issue
- 1
- Pages
- 361-396
- ISSN
- 1056-8700 (ISSN-L)
- 1545-4266
- OpenAlex
- W2130949317
- Cited by
- 341
- References
- 133
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 3 · 2023: 5 · 2022: 2 · 2021: 5 · 2020: 6 · 2019: 7 · 2018: 6 · 2017: 5 · 2016: 8 · 2015: 6 · 2014: 6 · 2013: 11 · 2012: 15
- FWCI
- 2.36
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Biophysics and Biomolecular Structure (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
- Keywords
- protein folding kinetics, nucleation theory, folding nucleus, transition state ensemble, protein evolution, molecular dynamics, lattice model
- MeSH terms
- Cell Nucleus, Kinetics, Models, Molecular, Monte Carlo Method, Thermodynamics, Protein Folding, Evolution, Molecular
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