The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Challenges in protein-folding simulations
Open accessAbstract
Experimental studies of protein folding processes are frequently hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.
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Cites
Current Status of the AMOEBA Polarizable Force Field
Ponder, J. W., Wu, C., Ren, P., Pande, V. S., Chodera, J. D., Schnieders, M. J., Haque, I., Mobley, D. L., Lambrecht, D. S., DiStasio, R. A., et al. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp910674d · Cited by 1,440
Designing a 20-residue protein
Neidigh, J. W., Fesinmeyer, R. M., & Andersen, N. H. (2002) · Nature Structural Biology · doi:10.1038/nsb798 · Cited by 793
Millisecond-scale molecular dynamics simulations on Anton
Shaw, D. E., Dror, R. O., Salmon, J. K., Grossman, J. P., Mackenzie, K. M., Bank, J. A., Young, C., Deneroff, M. M., Batson, B., Bowers, K. J., et al. (2009) · Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis · doi:10.1145/1654059.1654099 · Cited by 382
Cited by
How fast-folding proteins fold
Lindorff-Larsen, K., Piana, S., Dror, R. O., & Shaw, D. E. (2011) · Science · doi:10.1126/science.1208351 · Cited by 1,980
Molecular dynamics simulations and novel drug discovery
Liu, X., Shi, D., Zhou, S., Liu, H., Liu, H., & Yao, X. (2018) · Expert Opinion on Drug Discovery · doi:10.1080/17460441.2018.1403419 · Cited by 518
Structure and Response to Flow of the Glycocalyx Layer
Cruz-Chu, E. R., Malafeev, A., Pajarskas, T., Pivkin, I. V., & Koumoutsakos, P. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2013.09.060 · Cited by 87
Hierarchical Folding Free Energy Landscape of HP35 Revealed by Most Probable Path Clustering
Jain, A., & Stock, G. (2014) · The Journal of Physical Chemistry B · doi:10.1021/jp410398a · Cited by 48
Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations
(2023) · doi:10.1021/acs.jcim.3c01107 · Cited by 24
Metadata
- Authors
- Freddolino, L., Harrison, C. B., Liu, Y., & Schulten, K.
- Venue
- Nature Physics
- Published
- 2010-10
- Volume
- 6
- Issue
- 10
- Pages
- 751-758
- ISSN
- 1745-2473 (ISSN-L)
- 1745-2481
- OpenAlex
- W1964296596
- Cited by
- 329
- References
- 3
- FWCI
- 9.69
- Type
- journal article
- Language
- en
- Open access
- green
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