The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review
Abstract
Methods to search for low‐energy conformations, to generate a Boltzmann‐weighted ensemble of configurations, or to generate classical‐dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008
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Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
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
T RANSITION P ATH S AMPLING : Throwing Ropes Over Rough Mountain Passes, in the Dark
Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
Cited by
Lodewyk, M. W., Siebert, M. R., & Tantillo, D. J. (2012) · Chemical Reviews · doi:10.1021/cr200106v · Cited by 1,287
Coarse-Grained Protein Models and Their Applications
Kmiecik, S., Gront, D., Kolinski, M., Wieteska, L., Dawid, A. E., & Kolinski, A. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.6b00163 · Cited by 1,071
Perspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
Deng, Y., & Roux, B. (2009) · The Journal of Physical Chemistry B · doi:10.1021/jp807701h · Cited by 591
Piana, S., Klepeis, J. L., & Shaw, D. E. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2013.12.006 · Cited by 512
Metadata
- Authors
- Christen, M., & van Gunsteren, W. F.
- Venue
- Journal of Computational Chemistry
- Publisher
- Wiley
- Published
- 2007-06-14
- Volume
- 29
- Issue
- 2
- Pages
- 157-166
- ISSN
- 0192-8651 (ISSN-L)
- 1096-987X
- OpenAlex
- W2016856091
- Cited by
- 159
- References
- 3
- FWCI
- 3.83
- Type
- journal article
- Language
- en
- Open access
- closed
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- Christen, M., & van Gunsteren, W. F. (2008). On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. Journal of Computational Chemistry. https://doi.org/10.1002/jcc.20725
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