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

Min Li, John Zhang, Fei Xia

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)795-804
Number of pages10
JournalJournal of Computational Chemistry
Volume37
Issue number9
DOIs
StatePublished - Apr 5 2016

Fingerprint

Biomolecules
Optimization
Normal Modes
Biomaterials
Multiscale Simulation
Actin
Biocompatible Materials
Mechanical Properties
Actins
Computational Cost
Model
Fluctuations
Mechanical properties
Motion
Costs

Keywords

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

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

Cite this

A new algorithm for construction of coarse-grained sites of large biomolecules. / Li, Min; Zhang, John; Xia, Fei.

In: Journal of Computational Chemistry, Vol. 37, No. 9, 05.04.2016, p. 795-804.

Research output: Contribution to journalArticle

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