A 3-d coarser-grained computational model for simulating large Protein dynamics

Jae In Kim, Hyoseon Jang, Jeong Hee Ahn, Kilho Eom, Sungsoo Na

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Protein dynamics is essential for gaining insight into biological func- tions of proteins. Although protein dynamics is well delineated by molecular model, the molecular model is computationally prohibited for simulating large pro- tein structures. In this work, we provide the three-dimensional coarser-grained anisotropic model (CGAM), which is based on model reduction applicable to large protein structures. It is shown that CGAM achieves the fast computation on low- frequency modes, quantitatively comparable to original structural model such as elastic network model (ENM). This indicates that the by model reduction method enable us to understand the functional motion of large proteins with re- markable computational efficiency.

Original languageEnglish
Pages (from-to)137-151
Number of pages15
JournalComputers, Materials and Continua
Volume9
Issue number2
Publication statusPublished - 2009

Keywords

  • Coarser-grained anisotropic model
  • Elastic network model
  • Low-frequency mode
  • Protein dynamics

ASJC Scopus subject areas

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

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