Coarse grained modeling of biopolymers and proteins

Methods and applications

Dechang Li, Baohua Ji*, Kehchih Hwang, Yonggang Huang

*Corresponding author for this work

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Single-molecule mechanics of DNA/RNA, polypeptide and protein has become a new frontier in life sciences. There is an increasing need in participant of researcher in applied mechanics to perform a systematic study on methodologies and basic sciences in molecular mechanics. The wide-applied continuum mechanics may not be applicable in study of the biomolecules. At the same time, the all-atom molecular dynamics method is severely limited by the size and time scales of systems it can simulate. As an alternative, coarse-grained models have recently enjoyed intense interest. Coarse-grained representations combined with enhanced computer power currently allow the simulation of systems of biologically relevant size (submicrometric) and timescale (microsecond or millisecond). In this paper, we reported some progresses we made in the modeling of biomolecules using the coarse-grained methods including, the collapse of biopolymers, the dynamics of HIV-1 protease and the binding dynamics of inhibitors into the protease, aiming to stimulating a broader interest in developing molecular mechanics.

Original languageEnglish (US)
Pages (from-to)113-136
Number of pages24
JournalInternational Journal of Applied Mechanics
Volume1
Issue number1
DOIs
StatePublished - Mar 1 2009

Fingerprint

Molecular mechanics
Biopolymers
Biomolecules
Mechanics
Proteins
Continuum mechanics
Polypeptides
RNA
Molecular dynamics
DNA
Peptide Hydrolases
Atoms
Peptides
Molecules
Human immunodeficiency virus 1 p16 protease

Keywords

  • Coarse grained modeling
  • DNA
  • molecular dynamics simulation
  • molecular mechanics
  • protein

ASJC Scopus subject areas

  • Materials Science(all)
  • Mechanics of Materials
  • Mechanical Engineering

Cite this

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abstract = "Single-molecule mechanics of DNA/RNA, polypeptide and protein has become a new frontier in life sciences. There is an increasing need in participant of researcher in applied mechanics to perform a systematic study on methodologies and basic sciences in molecular mechanics. The wide-applied continuum mechanics may not be applicable in study of the biomolecules. At the same time, the all-atom molecular dynamics method is severely limited by the size and time scales of systems it can simulate. As an alternative, coarse-grained models have recently enjoyed intense interest. Coarse-grained representations combined with enhanced computer power currently allow the simulation of systems of biologically relevant size (submicrometric) and timescale (microsecond or millisecond). In this paper, we reported some progresses we made in the modeling of biomolecules using the coarse-grained methods including, the collapse of biopolymers, the dynamics of HIV-1 protease and the binding dynamics of inhibitors into the protease, aiming to stimulating a broader interest in developing molecular mechanics.",
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Coarse grained modeling of biopolymers and proteins : Methods and applications. / Li, Dechang; Ji, Baohua; Hwang, Kehchih; Huang, Yonggang.

In: International Journal of Applied Mechanics, Vol. 1, No. 1, 01.03.2009, p. 113-136.

Research output: Contribution to journalArticle

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