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J Chem Inf Model. 2010 May 24;50(5):792-800. doi: 10.1021/ci900508k.

LowModeMD--implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops.

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Chemical Computing Group, Inc., 1010 Sherbrooke St. W., Suite 910, Montreal H3A 2R7, Quebec, Canada.


We present a method for conformational search of complex molecular systems such as macrocycles and protein loops. The method is based on perturbing an existing conformation along a molecular dynamics trajectory using initial atomic velocities with kinetic energy concentrated on the low-frequency vibrational modes, followed by energy minimization. A novel Chebyshev polynomial filter is used to heavily dampen the high-frequency components of a randomly generated Maxwell-Boltzmann velocity vector. The method is very efficient, even for large systems; it is straightforward to implement and requires only standard force-field energy and gradient evaluations. The results of several computational experiments suggest that the method is capable of efficiently sampling low-strain energy conformations of complex systems with nontrivial nonbonded interaction networks.

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