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Extra info for Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods
With growing interest in protein dynamics there has been a rapid development both in hardware and software (methodology) to simulate conformational rearrangements and characterize structural ensembles, which has enabled increasing timescales and molecular size for studying dynamics. For example, owing to improved sampling techniques, multiscale approaches, and parallelization, folding dynamics simulations will soon attain millisecond timescales . , ribosome) [233,234]. Experimental techniques have advanced to determine conformational ensembles of proteins lacking a well-defined three-dimensional structure .
5. Brooks B, Karplus M (1985) Normal modes for specific motions of macromolecules: Application to the hinge-bending mode of lysozyme. Proc Natl Acad Sci U S A 82, 4995–4999. 6. Cao ZW, Chen X, Chen YZ (2003) Correlation between normal modes in the 20–200 cm-1 frequency range and localized torsio motions to certain collective motions in proteins. J Mol Graph Model 21, 309–319. 7. Ma J, Karplus M (1997) Ligand-induced conformational changes in ras p21: A normal mode and energy minimization analysis.
Consistency between the forces at the boundary are hence prerequisites for such developments. To answer questions at biologically relevant timescales, enhanced sampling has to be performed. Parallel simulations and exchanging information between multiple trajectories significantly increased the available configurational space. For long MD simulations the relaxation time of the system has to be considered and the dependency on the initial configurations also has to be probed. For enhanced sampling techniques, the main issue is the choice of the reaction coordinate along which the system is biased.