The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
Open accessAbstract
Hybrid computational methods for combining structural data from different sources and resolutions are becoming an essential part of structural biology, especially as the field moves toward the study of large macromolecular assemblies. We have developed the molecular dynamics flexible fitting (MDFF) method for combining high-resolution atomic structures with cryo-electron microscopy (cryo-EM) maps, that results in atomic models representing the conformational state captured by cryo-EM. The method has been applied successfully to the ribosome, a ribonucleoprotein complex responsible for protein synthesis. MDFF involves a molecular dynamics simulation in which a guiding potential, based on the cryo-EM map, is added to the standard force field. Forces proportional to the gradient of the density map guide an atomic structure, available from X-ray crystallography, into high-density regions of a cryo-EM map. In this paper we describe the necessary steps to set up, run, and analyze MDFF simulations and the software packages that implement the corresponding functionalities.
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VMD: visual molecular dynamics
Humphrey, W., Dalke, A., & Schulten, K. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00018-5 · Cited by 66,952
Self-citationScalable molecular dynamics with NAMD
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry · doi:10.1002/jcc.20289 · Cited by 16,914
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Cited by
Molecular Architecture of the SARS-CoV-2 Virus
Yao, H., Song, Y., Chen, Y., Wu, N., Xu, J., Sun, C., Zhang, J., Weng, T., Zhang, Z., Wu, Z., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.018 · Cited by 1,060
“Molecular dynamic flexible fitting (MDFF) (Trabuco et al., 2009) was applied to improve the fitting of the atomic model to the S in RBD down conformation.”
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics
Zhao, G., Perilla, J. R., Yufenyuy, E. L., Meng, X., Chen, B., Ning, J., Ahn, J., Gronenborn, A. M., Schulten, K., Aiken, C., et al. (2013) · Nature · doi:10.1038/nature12162 · Cited by 801
Self-citationCasX enzymes comprise a distinct family of RNA-guided genome editors
Liu, J.-J., Orlova, N., Oakes, B. L., Ma, E., Spinner, H. B., Baney, K. L. M., Chuck, J., Tan, D., Knott, G. J., Harrington, L. B., et al. (2019) · Nature · doi:10.1038/s41586-019-0908-x · Cited by 446
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
Schur, F. K. M., Hagen, W. J. H., Rumlová, M., Ruml, T., Müller, B., Kräusslich, H.-G., & Briggs, J. A. G. (2015) · Nature · doi:10.1038/nature13838 · Cited by 296
The SARS-CoV-2 Spike variant D614G favors an open conformational state
Mansbach, R. A., Chakraborty, S., Nguyen, K., Montefiori, D. C., Korber, B., & Gnanakaran, S. (2021) · Science Advances · doi:10.1126/sciadv.abf3671 · Cited by 206
Metadata
- Authors
- Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B., & Schulten, K.
- Venue
- Methods
- Publisher
- Elsevier BV
- Published
- 2009-10
- Volume
- 49
- Issue
- 2
- Pages
- 174-180
- ISSN
- 1046-2023 (ISSN-L)
- OpenAlex
- W2089638270
- Cited by
- 345
- References
- 2
- FWCI
- 9.38
- Type
- journal article
- Language
- en
- Open access
- green
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- Trabuco, L. G., Villa, E., Schreiner, E., Harrison, C. B., & Schulten, K. (2009). Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography. Methods. https://doi.org/10.1016/j.ymeth.2009.04.005
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