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issn:1757-594
1.  Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules 
The rugged energy landscape of biomolecules together with shortcomings of traditional molecular dynamics (MD) simulations require specialized methods for capturing large-scale, long-time configurational changes along with chemical dynamics behavior. In this report, MD-based methods for biomolecules are surveyed, involving modification of the potential, simulation protocol, or algorithm as well as global reformulations. While many of these methods are successful at probing the thermally accessible configuration space at the expense of altered kinetics, more sophisticated approaches like transition path sampling or Markov chain models are required to obtain mechanistic information, reaction pathways, and/or reaction rates. Divide-and-conquer methods for sampling and for piecing together reaction rate information are especially suitable for readily available computer cluster networks. Successful applications to biomolecules remain a challenge.
doi:10.3410/B1-51
PMCID: PMC2948272  PMID: 20948633
2.  Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure 
The rugged energy landscape of biomolecules and associated large-scale conformational changes have triggered the development of many innovative enhanced sampling methods, either based or not based on molecular dynamics (MD) simulations. Surveyed here are methods in the latter class - including Monte Carlo methods, harmonic approximations, and coarse graining - many of which yield valuable conformational insights into biomolecular structure and flexibility, despite altered kinetics. MD-based methods are surveyed in an upcoming issue of F1000 Biology Reports.
doi:10.3410/B1-48
PMCID: PMC2924683  PMID: 20948637

Results 1-2 (2)