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.
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University 251 Mercer Street, New York, NY 10012 USA. schlick@nyu.edu
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