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• W2289509599 abstract "Coarse-grained (CG) models are valuable tools for the study of functions of large biomolecules on large length and time scales. The definition of CG representations for huge biomolecules is always a formidable challenge. In this work, we propose a new method called fluctuation maximization coarse-graining (FM-CG) to construct the CG sites of biomolecules. The defined residual in FM-CG converges to a maximal value as the number of CG sites increases, allowing an optimal CG model to be rigorously defined on the basis of the maximum. More importantly, we developed a robust algorithm called stepwise local iterative optimization (SLIO) to accelerate the process of coarse-graining large biomolecules. By means of the efficient SLIO algorithm, the computational cost of coarse-graining large biomolecules is reduced to within the time scale of seconds, which is far lower than that of conventional simulated annealing. The coarse-graining of two huge systems, chaperonin GroEL and lengsin, indicates that our new methods can coarse-grain huge biomolecular systems with up to 10 000 residues within the time scale of minutes. The further parametrization of CG sites derived from FM-CG allows us to construct the corresponding CG models for studies of the functions of huge biomolecular systems." @default.
• W2289509599 created "2016-06-24" @default.
• W2289509599 creator A5017541012 @default.
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• W2289509599 date "2016-03-14" @default.
• W2289509599 modified "2023-10-14" @default.
• W2289509599 title "Constructing Optimal Coarse-Grained Sites of Huge Biomolecules by Fluctuation Maximization" @default.
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• W2289509599 doi "https://doi.org/10.1021/acs.jctc.6b00016" @default.
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• W2289509599 hasPublicationYear "2016" @default.
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