Computational techniques for efficient conformational sampling of proteins |
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Authors: | Liwo Adam Czaplewski Cezary O?dziej Stanis?aw Scheraga Harold A |
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Institution: | Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, United States. |
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Abstract: | In this review, we summarize the computational methods for sampling the conformational space of biomacromolecules. We discuss the methods applicable to find only lowest energy conformations (global minimization of the potential-energy function) and to generate canonical ensembles (canonical Monte Carlo method and canonical molecular dynamics method and their extensions). Special attention is devoted to the use of coarse-grained models that enable simulations to be enhanced by several orders of magnitude. |
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