The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Convergence of molecular dynamics simulations of membrane proteins
Abstract
The central question in evaluating almost any result from a molecular dynamics simulation is whether the calculation has converged. Unfortunately, assessing the ergodicity of a single trajectory is very difficult to do. In this work, we assess the sampling of molecular dynamics simulations of the membrane protein rhodopsin by comparing the results from 26 independent trajectories, each run for 100 ns. By examining principal components and cluster populations, we show that rhodopsin's fluctuations are not well described by 100 ns of dynamics, and that the sampling is not fully converged even for individual loops. The results serve as a reminder of the caution required when interpreting molecular dynamics simulations of macromolecules. Proteins 2007. © 2007 Wiley‐Liss, Inc.
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Cites
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Trong, I. L., Teller, D. C., Okada, T., Stenkamp, R. E., et al. (2000) · Science · doi:10.1126/science.289.5480.739 · Cited by 5,637
The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2 Å Crystal Structure
Okada, T., Sugihara, M., Bondar, A.-N., Elstner, M., Entel, P., & Buss, V. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.044 · Cited by 1,049
Cited by
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
Bahar, I., Lezon, T. R., Bakan, A., & Shrivastava, I. H. (2010) · Chemical Reviews · doi:10.1021/cr900095e · Cited by 537
Membrane proteins: molecular dynamics simulations
LINDAHL, E., & SANSOM, M. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.02.003 · Cited by 314
Metadata
- Authors
- Grossfield, A., Feller, S. E., & Pitman, M. C.
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2007-01-22
- Volume
- 67
- Issue
- 1
- Pages
- 31-40
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W1976993208
- Cited by
- 172
- References
- 2
- FWCI
- 6.82
- Type
- journal article
- Language
- en
- Open access
- closed
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