The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
All-Atom Structure Prediction and Folding Simulations of a Stable Protein
Abstract
We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.
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Citations
Cites
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
Cited by
The Amber biomolecular simulation programs
Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., & Woods, R. J. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20290 · Cited by 9,535
Self-citationOnufriev, A., Bashford, D., & Case, D. A. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20033 · Cited by 2,507
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
Trp-cage: Folding free energy landscape in explicit water
Zhou, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2233312100 · Cited by 363
Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins
Pitera, J. W., & Swope, W. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1330954100 · Cited by 344
Metadata
- Authors
- Simmerling, C., Strockbine, B., & Roitberg, A. E.
- Venue
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-08-28
- Volume
- 124
- Issue
- 38
- Pages
- 11258-11259
- ISSN
- 0002-7863 (ISSN-L)
- 1520-5126
- OpenAlex
- W2042490093
- Cited by
- 589
- References
- 1
- FWCI
- 11.02
- Type
- journal article
- Language
- en
- Open access
- closed
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- Simmerling, C., Strockbine, B., & Roitberg, A. E. (2002). All-Atom Structure Prediction and Folding Simulations of a Stable Protein. Journal of the American Chemical Society. https://doi.org/10.1021/ja0273851
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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.
