Dr. Evelyne Deplazes: Difference between revisions
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'''email''' e.deplazes@uq.edu.au | '''email''' e.deplazes@uq.edu.au | ||
== Biography == | |||
I completed a double degree in Chemistry and Computer Science at Curtin University in Perth (2003-2006). During my undergraduate research project I used quantum chemical calculations to simulate the to IR and Raman spectra of histidine in solution. The results are used by other researchers as a reference to distinguish between the different protonation states of histidine. After that I completed an Honours in Computational Chemistry (2007) focusing on quantum mechanical calculations of transition metals for modelling the chemical and physical properties of materials. | |||
In 2008 I was awarded my PhD in Computational Biophysics from the University of Western Australia, Perth. As part of my PhD I have developed methods for integrating structural data from spectroscopy experiments into simulations to model the gating behavior of mechanosensitive ion channels that predicted the role of specific structural domains in the gating mechanism of the channel. Furthermore, my PhD project focused on using molecular dynamics and Monte Carlo simulations to aid in the analysis and interpretation of FRET spectroscopy experiments. | |||
After finishing my PhD I joined the research groups of Prof. Alan Mark (School of Chemistry and Molecular Biosciences, UQ) and Prof. Glenn King (Institute for Molecular Bioscience, UQ) to work on a collaborative project that focuses on peptides derived from animal venoms for the development of new drugs to treat chronic pain. | |||
== Research Interests and Projects == | |||
My main research area is the use of computational chemistry for investigating the structure-activity relationship of ion channels and their interactions with drug molecules. This allows me to integrate my knowledge and skills in chemistry, structural biology and computer science. I am experienced in a range of molecular modelling techniques and theoretical approaches including quantum mechanical calculations, Monte Carlo simulations, molecular dynamics simulations, homology modelling and docking. In addition I am interested in the developing computational methods that enables researchers to make better use of the data from spectroscopy experiment, with a particular focus on FRET and EPR. <br> | |||
Development of venom-based drugs for treating chronic pain | |||
This project is a collaboration between the MD group at the School of Chemistry and Molecular Biosciences (UQ) and the King group | |||
The project combines molecular dynamics simulations and docking with experimental validation to characterize the interactions between the venom peptides and acid sensing ion channels. The results from the simulations will aid the optimization of the peptides into small-molecule analgesics that might be more useful therapeutically. | |||
== Publications == | |||
</p> | |||
<h4>Book Chapters</h4> | |||
<p> | |||
1. Deplazes E., O’Mara M.L., 2014, Polypeptide and Protein Modeling for Drug Design, Encyclopaedia of Computational Neuroscience (accepted for publication) </br> | |||
</p> | |||
<h4>Refereed Journal Articles</h4> | |||
1. *Deplazes E. , Louhivuori M., Jayatilaka D., Marrink SJ., Corry B., 2012, Structural investigation of MscL gating using experimental data and coarse grained MD simulations, PloS Computational Biology, vol 8, issue 9 </br> | |||
2. Martinac B. , Petrov E., Cranfield CG, Nomura T., Rhode PR., Battle AR., Landsberg JL, Foo A. Constatine M, Rothnagel R., Carne S., Chi G., Deplazes E., Cronell B., Hankammer, B., 2012, Bacterial mechansosensitive ion channels (Review), accepted for publication in Antioxidant & Redox signalling | |||
3. Nomura T., Cranfield CG, Deplazes E., Owen DM., Macmillan A., Battle AR, Constantine M., Sokabe M., Martinac B. 2012, Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS, PNAS, vol 109 (122), 8770-8775 </br> | |||
4. *Deplazes E., Jayatilaka D and Corry B., 2011, Testing the use of molecular dynamics to simulate fluorophore motions and FRET, Physcial Chemistry Chemcial Physics, 13 (23), 11045-11054 </br> | |||
5. Deplazes E., Jayatilaka D and Corry B., 2011, ExiFRET: A flexible tool for understanding FRET in complex geometries, Journal of Biomedical Optics, 17, 011005 </br> | |||
6. Deplazes E., van Bronswijk W., Zhu F., Barron L.D. , Ma S., Nafi A. and Jalkanen K.J., 2010, A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L -histidine zwitterion, Theoretical Chemistry Accounts, Vol. 19, no. 1-3, pp. 155 – 176</br> | |||
7. Varganov S.A., Gilbert A.T., Deplazes E., Gill P.M., 2008, Resolution of the Coloumb operator, Journal of Chemical Physics, Vol. 128, no. 20, pp. 201104 </br> | |||
Revision as of 04:09, 8 January 2014
Contact Details
Dr. Evelyne Deplazes
Molecular Dynamics Group
School of Chemistry and Molecular Biosciences (SCMB)
Molecular Biosciences Building (#76)
The University of Queensland
St. Lucia, Brisbane
QLD 4072
Australia
email e.deplazes@uq.edu.au
Biography
I completed a double degree in Chemistry and Computer Science at Curtin University in Perth (2003-2006). During my undergraduate research project I used quantum chemical calculations to simulate the to IR and Raman spectra of histidine in solution. The results are used by other researchers as a reference to distinguish between the different protonation states of histidine. After that I completed an Honours in Computational Chemistry (2007) focusing on quantum mechanical calculations of transition metals for modelling the chemical and physical properties of materials.
In 2008 I was awarded my PhD in Computational Biophysics from the University of Western Australia, Perth. As part of my PhD I have developed methods for integrating structural data from spectroscopy experiments into simulations to model the gating behavior of mechanosensitive ion channels that predicted the role of specific structural domains in the gating mechanism of the channel. Furthermore, my PhD project focused on using molecular dynamics and Monte Carlo simulations to aid in the analysis and interpretation of FRET spectroscopy experiments. After finishing my PhD I joined the research groups of Prof. Alan Mark (School of Chemistry and Molecular Biosciences, UQ) and Prof. Glenn King (Institute for Molecular Bioscience, UQ) to work on a collaborative project that focuses on peptides derived from animal venoms for the development of new drugs to treat chronic pain.
Research Interests and Projects
My main research area is the use of computational chemistry for investigating the structure-activity relationship of ion channels and their interactions with drug molecules. This allows me to integrate my knowledge and skills in chemistry, structural biology and computer science. I am experienced in a range of molecular modelling techniques and theoretical approaches including quantum mechanical calculations, Monte Carlo simulations, molecular dynamics simulations, homology modelling and docking. In addition I am interested in the developing computational methods that enables researchers to make better use of the data from spectroscopy experiment, with a particular focus on FRET and EPR.
Development of venom-based drugs for treating chronic pain This project is a collaboration between the MD group at the School of Chemistry and Molecular Biosciences (UQ) and the King group
The project combines molecular dynamics simulations and docking with experimental validation to characterize the interactions between the venom peptides and acid sensing ion channels. The results from the simulations will aid the optimization of the peptides into small-molecule analgesics that might be more useful therapeutically.
Publications
Book Chapters
1. Deplazes E., O’Mara M.L., 2014, Polypeptide and Protein Modeling for Drug Design, Encyclopaedia of Computational Neuroscience (accepted for publication)
Refereed Journal Articles
1. *Deplazes E. , Louhivuori M., Jayatilaka D., Marrink SJ., Corry B., 2012, Structural investigation of MscL gating using experimental data and coarse grained MD simulations, PloS Computational Biology, vol 8, issue 9
2. Martinac B. , Petrov E., Cranfield CG, Nomura T., Rhode PR., Battle AR., Landsberg JL, Foo A. Constatine M, Rothnagel R., Carne S., Chi G., Deplazes E., Cronell B., Hankammer, B., 2012, Bacterial mechansosensitive ion channels (Review), accepted for publication in Antioxidant & Redox signalling
3. Nomura T., Cranfield CG, Deplazes E., Owen DM., Macmillan A., Battle AR, Constantine M., Sokabe M., Martinac B. 2012, Differential effects of lipids and lyso-lipids on the mechanosensitivity of the mechanosensitive channels MscL and MscS, PNAS, vol 109 (122), 8770-8775
4. *Deplazes E., Jayatilaka D and Corry B., 2011, Testing the use of molecular dynamics to simulate fluorophore motions and FRET, Physcial Chemistry Chemcial Physics, 13 (23), 11045-11054
5. Deplazes E., Jayatilaka D and Corry B., 2011, ExiFRET: A flexible tool for understanding FRET in complex geometries, Journal of Biomedical Optics, 17, 011005
6. Deplazes E., van Bronswijk W., Zhu F., Barron L.D. , Ma S., Nafi A. and Jalkanen K.J., 2010, A combined theoretical and experimental study of the structure and vibrational absorption, vibrational circular dichroism, Raman and Raman optical activity spectra of the L -histidine zwitterion, Theoretical Chemistry Accounts, Vol. 19, no. 1-3, pp. 155 – 176
7. Varganov S.A., Gilbert A.T., Deplazes E., Gill P.M., 2008, Resolution of the Coloumb operator, Journal of Chemical Physics, Vol. 128, no. 20, pp. 201104
