Application of component mode synthesis to protein structure for dynamic analysis

Jae I. Kim, Kilho Eom, Moon Kyu Kwak, Sung Soo Na

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

This paper concerns the application of component mode synthesis for biomolecule modeling to understand protein dynamics. As for protein dynamics, eigenvalue problem should be formulated to obtain eigenvalue, eigenvector and thermal fluctuation. To describe the thermal fluctuation of protein, normal mode analysis is introduced and normal modes identify the dynamic behavior of protein very well. Component mode synthesis considers the given complex structure as an assembly of smaller components. The selection of a component may be arbitrary. When the component mode synthesis is applied to formulate the eigenvalue problem of protein structure, we selected a protein which may be composed of two and/or four domains. The domain of protein can be considered as a component. In this sense the number of component is increased as necessary, and the size of each component is decreased for fast calculation. The component mode synthesis widely used in engineering was well applied to understand protein dynamics in present study.

Original languageEnglish
Pages (from-to)67-73
Number of pages7
JournalComputers, Materials and Continua
Volume8
Issue number2
Publication statusPublished - 2008 Dec 1

Fingerprint

Component Mode Synthesis
Protein Structure
Dynamic Analysis
Dynamic analysis
Proteins
Protein
Normal Modes
Eigenvalue Problem
Fluctuations
Biomolecules
Eigenvalues and Eigenvectors
Number of Components
Complex Structure
Dynamic Behavior
Eigenvalues and eigenfunctions
Engineering
Necessary
Arbitrary

Keywords

  • Component mode synthesis
  • Eigenvalue problem
  • Normal mode analysis
  • Protein
  • Thermal fluctuation

ASJC Scopus subject areas

  • Computer Science Applications
  • Electrical and Electronic Engineering
  • Mechanics of Materials
  • Biomaterials
  • Modelling and Simulation

Cite this

Application of component mode synthesis to protein structure for dynamic analysis. / Kim, Jae I.; Eom, Kilho; Kwak, Moon Kyu; Na, Sung Soo.

In: Computers, Materials and Continua, Vol. 8, No. 2, 01.12.2008, p. 67-73.

Research output: Contribution to journalArticle

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