Coarse-grained modeling

Coarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules[1][2] at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins,[1][2] nucleic acids,[3][4] lipid membranes,[2][5] carbohydrates[6] or water.[7] In these models, molecules are represented not by individual atoms, but by "pseudo-atoms" approximating groups of atoms, such as whole amino acid residue. By decreasing the degrees of freedom much longer simulation times can be studied at the expense of molecular detail. Coarse-grained models have found practical applications in molecular dynamics simulations.[1]

The coarse-grained modeling originates from work by Michael Levitt and Ariel Warshel in 1970s.[8][9][10] Coarse-grained models are presently often used as components of multiscale modeling protocols in combination with reconstruction tools[11] (from coarse-grained to atomistic representation) and atomistic resolution models.[1] Atomistic resolution models alone are presently not efficient enough to handle large system sizes and simulation timescales.[1][2]


Software packages
  • Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
  • Extensible Simulation Package for Research on Soft Matter ESPReSo (external link)

References
  1. Kmiecik, Sebastian; Gront, Dominik; Kolinski, Michal; Wieteska, Lukasz; Dawid, Aleksandra Elzbieta; Kolinski, Andrzej (2016-06-22). "Coarse-Grained Protein Models and Their Applications". Chemical Reviews. 116 (14): 7898–936. doi:10.1021/acs.chemrev.6b00163. ISSN 0009-2665. PMID 27333362.
  2. Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.; de Jong, Djurre H.; Gopal, Srinivasa M.; Periole, Xavier; Marrink, Siewert J. (2014-05-01). "The power of coarse graining in biomolecular simulations". Wiley Interdisciplinary Reviews: Computational Molecular Science. 4 (3): 225–248. doi:10.1002/wcms.1169. ISSN 1759-0884. PMC 4171755. PMID 25309628.
  3. Boniecki, Michal J.; Lach, Grzegorz; Dawson, Wayne K.; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M.; Bujnicki, Janusz M. (2016-04-20). "SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction". Nucleic Acids Research. 44 (7): e63. doi:10.1093/nar/gkv1479. ISSN 0305-1048. PMC 4838351. PMID 26687716.
  4. Potoyan, Davit A.; Savelyev, Alexey; Papoian, Garegin A. (2013-01-01). "Recent successes in coarse-grained modeling of DNA". Wiley Interdisciplinary Reviews: Computational Molecular Science. 3 (1): 69–83. doi:10.1002/wcms.1114. ISSN 1759-0884. S2CID 12043343.
  5. Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H.; Elsener, Andreas; Marrink, Siewert J.; van Gunsteren, Wilfred F. (2007-02-19). "Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models" (PDF). ChemPhysChem. 8 (3): 452–461. doi:10.1002/cphc.200600658. ISSN 1439-7641. PMID 17290360.
  6. López, Cesar A.; Rzepiela, Andrzej J.; de Vries, Alex H.; Dijkhuizen, Lubbert; Hünenberger, Philippe H.; Marrink, Siewert J. (2009-12-08). "Martini Coarse-Grained Force Field: Extension to Carbohydrates". Journal of Chemical Theory and Computation. 5 (12): 3195–3210. doi:10.1021/ct900313w. ISSN 1549-9618. PMID 26602504.
  7. Hadley, Kevin R.; McCabe, Clare (2012-07-01). "Coarse-grained molecular models of water: a review". Molecular Simulation. 38 (8–9): 671–681. doi:10.1080/08927022.2012.671942. ISSN 0892-7022. PMC 3420348. PMID 22904601.
  8. Levitt, Michael; Warshel, Arieh (1975-02-27). "Computer simulation of protein folding". Nature. 253 (5494): 694–698. doi:10.1038/253694a0. PMID 1167625.
  9. Warshel, A.; Levitt, M. (1976-05-15). "Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme". Journal of Molecular Biology. 103 (2): 227–249. doi:10.1016/0022-2836(76)90311-9. ISSN 0022-2836. PMID 985660.
  10. Levitt, Michael (2014-09-15). "Birth and Future of Multiscale Modeling for Macromolecular Systems (Nobel Lecture)". Angewandte Chemie International Edition. 53 (38): 10006–10018. doi:10.1002/anie.201403691. ISSN 1521-3773. PMID 25100216. S2CID 3680673.
  11. Badaczewska-Dawid, Aleksandra E.; Kolinski, Andrzej; Kmiecik, Sebastian (2020). "Computational reconstruction of atomistic protein structures from coarse-grained models". Computational and Structural Biotechnology Journal. 18: 162–176. doi:10.1016/j.csbj.2019.12.007. ISSN 2001-0370. PMC 6961067. PMID 31969975.
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