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research article

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

Dal Peraro, M.  
•
Ruggerone, P.
•
Raugei, S.
Show more
2007
Current Opinion in Structural Biology

Density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations describe the time evolution of molecular systems without resorting to a predefined potential energy surface. CPMD and hybrid molecular mechanics/CPMD schemes have recently enabled the calculation of redox properties of electron transfer proteins in their complex biological environment. They provided structural and spectroscopic information on novel platinum-based anticancer drugs that target DNA, also setting the basis for the construction of force fields for the metal lesion. Molecular mechanics/CPMD also lead to mechanistic hypotheses for a variety of metalloenzymes. Recent advances that increase the accuracy of DFT and the efficiency of investigating rare events are further expanding the domain of CPMD applications to biomolecules.

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Type
research article
DOI
10.1016/j.sbi.2007.03.018
Author(s)
Dal Peraro, M.  
Ruggerone, P.
Raugei, S.
Gervasio, F. L.
Carloni, P.
Date Issued

2007

Published in
Current Opinion in Structural Biology
Volume

17

Issue

2

Start page

149

End page

56

Subjects

Antineoplastic Agents/chemistry

•

Electrochemistry

•

Electron Transport

•

Enzymes/chemistry

•

Ligands

•

Metalloproteins/chemistry

•

Models

•

Biological

•

Models

•

Molecular

•

Oxidation-Reduction

•

Platinum Compounds/chemistry

•

*Systems Biology

•

*Thermodynamics

Note

Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
UPDALPE  
Available on Infoscience
April 28, 2008
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/23508
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