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Curr Opin Struct Biol. 2006 Apr;16(2):160-5. Epub 2006 Feb 17.

Conformer generation under restraints.

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  • 1Department of Molecular Biology and Center for Human Genetic Research, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114-2790, USA.

Abstract

Conformational sampling by direct optimization of an all-atom energy function is ineffective and inefficient because of the ruggedness of the energy landscape. Discrete sampling schemes represent an attractive alternative for generating ensembles of conformers consistent with spatial restraints derived from empirical data. Conformational sampling is becoming increasingly important for structure prediction as the bottleneck in accurate prediction shifts from energy functions to the methods used to find low-energy conformers. Experimental structure determination remains a perennial challenge as investigators tackle larger macromolecular systems, and begin to incorporate more complete descriptions of uncertainty, heterogeneity and dynamics into their models. Computational approaches that combine dense, discrete sampling with all-atom energy evaluation and refinement may help to overcome the remaining barriers to solving these problems.

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