On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.

@article{citeulike:1394953, abstract = {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. (c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.}, address = {Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Z\"{u}rich, ETH, CH‐8093 Z\"{u}rich, Switzerland.}, author = {Christen, Markus and van Gunsteren, Wilfred F F. }, citeulike-article-id = {1394953}, doi = {http://dx.doi.org/10.1002/jcc.20725}, issn = {0192-8651}, journal = {J Comput Chem}, keywords = {conformation, docking}, month = {June}, posted-at = {2007-06-17 20:59:32}, priority = {3}, title = {On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.}, url = {http://dx.doi.org/10.1002/jcc.20725}, year = {2007} }

TY - JOUR ID - citeulike:1394953 L3 - citeulike-article-id:1394953 TI - On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review. JF - J Comput Chem AD - Laboratory of Physical Chemistry, Swiss Federal Institute of Technology Zürich, ETH, CH‐8093 Zürich, Switzerland. SN - 0192-8651 N2 - 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. (c) 2007 Wiley Periodicals, Inc. J Comput Chem, 2007. KW - conformation KW - docking AU - Christen, Markus AU - van Gunsteren, Wilfred F PY - 2007/06/14/ UR - http://dx.doi.org/10.1002/jcc.20725 ER -