Atomistic Molecular Dynamics provides powerful and flexible tools for the prediction and analysis of molecular and macromolecular systems. Specifically, it provides a means by which we can measure theoretically that which cannot be measured experimentally: the dynamic time-evolution of complex systems comprising atoms and molecules. It is particularly suitable for the simulation and analysis of the otherwise inaccessible details of MHC-peptide interaction and, on a larger scale, the simulation of the immune synapse. Progress has been relatively tentative yet the emergence of truly high-performance computing and the development of coarse-grained simulation now offers us the hope of accurately predicting thermodynamic parameters and of simulating not merely a handful of proteins but larger, longer simulations comprising thousands of protein molecules and the cellular scale structures they form. We exemplify this within the context of immunoinformatics.
Bibliographical note© 2010 Flower et al; licensee BioMed Central Ltd.
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- atomistic molecular dynamics
- molecular systems
- macromolecular systems
Flower, D. R., Phadwal, K., Macdonald, I. K., Coveney, P. V., Davies, M. N., & Wan, S. (2010). T-cell epitope prediction and immune complex simulation using molecular dynamics: state of the art and persisting challenges. Immunome Research, 6(Suppl.2), S4. [S4]. https://doi.org/10.1186/1745-7580-6-S2-S4