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Chem Rev. 2016 Jul 27;116(14):7898-936. doi: 10.1021/acs.chemrev.6b00163. Epub 2016 Jun 22.

Coarse-Grained Protein Models and Their Applications.

Author information

1
Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warsaw, Poland.
2
Bioinformatics Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences , Pawinskiego 5, 02-106 Warsaw, Poland.
3
Department of Medical Biochemistry, Medical University of Lodz , Mazowiecka 6/8, 92-215 Lodz, Poland.

Abstract

The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies.

PMID:
27333362
DOI:
10.1021/acs.chemrev.6b00163
[Indexed for MEDLINE]
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