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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
