alexa Molecular Dynamics Simulation of Proteins: A Brief Overview | OMICS International| Abstract

ISSN: 2161-0398

Journal of Physical Chemistry & Biophysics

  • Review Article   
  • J Phys Chem Biophys 2014, Vol 4(6): 166
  • DOI: 10.4172/2161-0398.1000166

Molecular Dynamics Simulation of Proteins: A Brief Overview

Sachin Patodia1, Ashima Bagaria1* and Deepak Chopra2*
1Centre for Converging Technologies, University of Rajasthan, Jaipur 302004, Rajasthan, India
2Department of Chemistry, Indian Institute of Science Education and Research, , Bhopal 462066, India
*Corresponding Author (s) : Ashima Bagaria, Centre for Converging Technologies, University of Rajasthan, Jaipur 302004, Rajasthan, India, Tel: 0755-6692-370, Email: [email protected]
Deepak Chopra, Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462066, India, Tel: 0755-6692-370, Email: [email protected]

Received Date: Oct 04, 2014 / Accepted Date: Oct 28, 2014 / Published Date: Oct 31, 2014

Abstract

MD simulation has become an essential tool for understanding the physical basis of the structure of proteins and their biological functions. During the current decade we witnessed significant progress in MD simulation of proteins with advancement in atomistic simulation algorithms, force fields, computational methods and facilities, comprehensive analysis and experimental validation, as well as integration in wide area bioinformatics and structural/systems biology frameworks. In this review, we present the methodology on protein simulations and recent advancements in the field. MD simulation provides a platform to study protein–protein, protein–ligand and protein–nucleic acid interactions. MD simulation is also done with NMR relaxation timescale in order to get residual dipolar coupling and order parameter of protein molecules.

Keywords: Molecular dynamics simulation; Force field; Residual dipolar coupling; Orders parameter

Citation: Patodia S, Bagaria A, Chopra D (2014) Molecular Dynamics Simulation of Proteins: A Brief Overview. J Phys Chem Biophys 4: 166. Doi: 10.4172/2161-0398.1000166

Copyright: © 2014 Patodia S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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