On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.
Methods to search for low-energy conformations, to generate a Boltzmann-weighted ensemble of configurations, or to generate classical-dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest.
Christen
Markus
M
Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, CH-8093 Zürich, Switzerland.
van Gunsteren
Wilfred F
WF
D000465:Algorithms; D001709:Biotechnology / Q000379:methods*; D003198:Computer Simulation; D004735:Energy Transfer; D008968:Molecular Conformation; D013816:Thermodynamics