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J Comput Chem. 2016 Apr 5;37(9):795-804. doi: 10.1002/jcc.24265. Epub 2015 Dec 15.

A new algorithm for construction of coarse-grained sites of large biomolecules.

Li M1, Zhang JZ1,2, Xia F2,3.

Author information

1
State Key Laboratory of Precision Spectroscopy and Department of Physics, East China Normal University, Shanghai, 200062, China.
2
NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
3
School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.

Abstract

The development of coarse-grained (CG) models for large biomolecules remains a challenge in multiscale simulations, including a rigorous definition of CG representations for them. In this work, we proposed a new stepwise optimization imposed with the boundary-constraint (SOBC) algorithm to construct the CG sites of large biomolecules, based on the s cheme of essential dynamics CG. By means of SOBC, we can rigorously derive the CG representations of biomolecules with less computational cost. The SOBC is particularly efficient for the CG definition of large systems with thousands of residues. The resulted CG sites can be parameterized as a CG model using the normal mode analysis based fluctuation matching method. Through normal mode analysis, the obtained modes of CG model can accurately reflect the functionally related slow motions of biomolecules. The SOBC algorithm can be used for the construction of CG sites of large biomolecules such as F-actin and for the study of mechanical properties of biomaterials.

KEYWORDS:

ENM-ED-CG; coarse-grained representation; elastic network model

PMID:
26668124
DOI:
10.1002/jcc.24265
[Indexed for MEDLINE]

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