Molecular Dynamics: The Computational Molecular Microscope

Authors Information
Article Notes and Dates
To Cite : Reza Kalani M, Tajkhorshid E. Molecular Dynamics: The Computational Molecular Microscope, Razavi Int J Med. 2014 ;2(3):e20117. doi: 10.5812/rijm.20117.
Copyright: Copyright © 2014, Razavi International Journal of Medicine. .
1. Introduction
2. Molecular Modeling
3. Molecular Dynamics Simulation
4. Verification and Analysis of MD Simulations
5. Conclusions
  • 1. Tajkhorshid E, Aksimentiev A, Balabin I, Gao M, Isralewitz B, Phillips JC, et al. Large scale simulation of protein mechanics and function. Adv Protein Chem. 2003; 66: 195-247[PubMed]
  • 2. Loretz M, Pezzagna S, Meijer J, Degen CL. Nanoscale nuclear magnetic resonance with a 1.9-nm-deep nitrogen-vacancy sensor. Appl Phys Let. 2014; 104(3)
  • 3. Truong K, Ikura M. The use of FRET imaging microscopy to detect protein-protein interactions and protein conformational changes in vivo. Curr Opin Struct Biol. 2001; 11(5): 573-8[PubMed]
  • 4. Tajkhorshid E, Jalkanen KJ, Suhai S. Structure and Vibrational Spectra of the Zwitterion l-Alanine in the Presence of Explicit Water Molecules:  A Density Functional Analysis. J Phys Chem B. 1998; 102(30): 5899-913[DOI]
  • 5. Karimian SMH, Izadi S, Farimani AB. A study on the measurement of mean velocity and its convergence in molecular dynamics simulations. Int J Numer Methods Fluids. 2011; 67(12): 2130-40[DOI]
  • 6. Kalani MR, Moradi A, Moradi M, Tajkhorshid E. Characterizing a histidine switch controlling pH-dependent conformational changes of the influenza virus hemagglutinin. Biophys J. 2013; 105(4): 993-1003[PubMed]
  • 7. Alder BJ, Wainwright TE. Studies in Molecular Dynamics. I. General Method. J Chem Phys. 1959; 31(2): 459-66
  • 8. Karplus M, Petsko GA. Molecular dynamics simulations in biology. Nature. 1990; 347(6294): 631-9[DOI][PubMed]
Creative Commons License Except where otherwise noted, this work is licensed under Creative Commons Attribution Non Commercial 4.0 International License .

Search Relations:



Create Citiaion Alert via Google Reader

Cited By: