Computational techniques for efficient conformational sampling of proteins
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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Adam Liwo1, Cezary Czaplewski, Stanisław Ołdziej
1Baker Laboratory of Chemistry, Cornell University, Ithaca, NY 14853-1301, United States.
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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