The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Reconstruction of atomistic details from coarse‐grained structures
Open accessAbstract
We present an algorithm to reconstruct atomistic structures from their corresponding coarse‐grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low‐energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed‐phase biomolecular systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010
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Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Coarse Grained Model for Semiquantitative Lipid Simulations
Marrink, S. J., de Vries, A. H., & Mark, A. E. (2004) · The Journal of Physical Chemistry B · doi:10.1021/jp036508g · Cited by 2,257
Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations
Harmandaris, V. A., Adhikari, N. P., van der Vegt, N. F. A., & Kremer, K. (2006) · Macromolecules · doi:10.1021/ma0606399 · Cited by 350
Milano, G., & Müller-Plathe, F. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp0523571 · Cited by 260
Spyriouni, T., Tzoumanekas, C., Theodorou, D., Müller-Plathe, F., & Milano, G. (2007) · Macromolecules · doi:10.1021/ma0700983 · Cited by 204
Long time atomistic polymer trajectories from coarse grained simulations: Bisphenol-A polycarbonate
Hess, B., León, S., van der Vegt, N., & Kremer, K. (2006) · Soft Matter · doi:10.1039/b602076c · Cited by 128
Cited by
The power of coarse graining in biomolecular simulations
Ingólfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014) · WIREs Computational Molecular Science · doi:10.1002/wcms.1169 · Cited by 572
Self-citationClassical Electrostatics for Biomolecular Simulations
Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2014) · Chemical Reviews · doi:10.1021/cr300461d · Cited by 259
CG2AT2: An enhanced fragment-based approach for serial multi-scale molecular dynamics simulations
Vickery, O. N., & Stansfeld, P. J. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00295 · Cited by 150
Mechanics of membrane fusion/pore formation
Fuhrmans, M., Marelli, G., Smirnova, Y. G., & Müller, M. (2015) · Chemistry and Physics of Lipids · doi:10.1016/j.chemphyslip.2014.07.010 · Cited by 65
Periole, X. (2017) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00344 · Cited by 58
Metadata
- Authors
- Rzepiela, A. J., Schäfer, L. V., Goga, N., Risselada, H. J., De Vries, A. H., & Marrink, S. J.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2010-01-19
- Volume
- 31
- Issue
- 6
- Pages
- 1333-1343
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2031163353
- Cited by
- 190
- References
- 6
- FWCI
- 6.50
- Type
- journal article
- Language
- en
- Open access
- bronze
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