Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/105599
Title: Multiscale coarse-graining via normal mode analysis
Authors: Xia, Fei
Lu, Lanyuan
Keywords: DRNTU::Science::Biological sciences
Issue Date: 2012
Source: Xia, F., & Lu, L. (2012). Multiscale coarse-graining via normal mode analysis. Journal of chemical theory and computation, 8(11), 4797-4806.
Series/Report no.: Journal of chemical theory and computation
Abstract: A multiscale coarse-graining method called the normal-mode analysis based fluctuation matching (NMA-FM) is developed for constructing coarse-grained models of biomolecular systems. In the framework of normal-mode analysis, an arbitrary fine-grained model can be systematically converted to a more coarse-grained model, while the crucial low-frequency motions of the fine-grained system are able to be reproduced in the coarse-grained modeling. The method relies on the technique of fluctuation matching that has been devised earlier for parametrizing heterogeneous elastic network models based on data from atomistic molecular dynamics simulations. The new approach is quite efficient since it avoids expensive atomistic molecular dynamics simulations and can start from already coarse-grained elastic network models. In the practical aspect, the method is suitable for conformational analyses of large biomacromolecules and calculations of mechanical properties of biomaterials, which is demonstrated by the studied systems including an amyloid dimer, lysozyme and adenylate kinase proteins, and the S2 subdomain of myosin.
URI: https://hdl.handle.net/10356/105599
http://hdl.handle.net/10220/17927
DOI: 10.1021/ct3006387
Fulltext Permission: none
Fulltext Availability: No Fulltext
Appears in Collections:SBS Journal Articles

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