TCB Publications - Abstract

Peter L. Freddolino, Anton Arkhipov, Amy Y. Shih, Ying Yin, Zhongzhou Chen, and Klaus Schulten. Application of residue-based and shape-based coarse graining to biomolecular simulations. In Gregory A. Voth, editor, Coarse-Graining of Condensed Phase and Biomolecular Systems, chapter 20, pp. 299-315. Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.

FRED2008 A wide variety of coarse-graining methods for biological systems currently exist, ranging in some sense from united-atom models to elastic network models. We focus on the principles and applications of two classes of biological coarse-graining, namely residue-based and shape-based coarse graining. Residue-based CG is a broad family of methods in which clusters of 10-20 covalently bonded atoms are represented by one bead; it is a fairly natural and common method for coarse-graining when a speedup of 1-2 orders of magnitude over all-atom simulations is required. Shape-based CG is a method recently developed in our group which uses a neural network algorithm to assign CG beads to domains of a protein, efficiently reproducing the shape of the protein with a minimal number of particles. Interactions between beads are then parameterized from all-atom simulations of the bead components. In this chapter we present a summary of both methods, along with exemplary applications of residue-based CG to two lipid-protein systems involving large-scale conformational changes, and of shape-based CG to the mechanical properties of polymeric systems.

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