Overview
Availability
- Dr Martin Stroet is:
- Available for supervision
Fields of research
Qualifications
- Bachelor of Science, The University of Queensland
- Doctor of Philosophy, The University of Queensland
Works
Search Professor Martin Stroet’s works on UQ eSpace
Featured
2022
Journal Article
PyThinFilm: Automated molecular dynamics simulation protocols for the generation of thin film morphologies
Stroet, Martin, Sanderson, Stephen, Sanzogni, Audrey V., Nada, Sharif, Lee, Thomas, Caron, Bertrand, Mark, Alan E. and Burn, Paul L. (2022). PyThinFilm: Automated molecular dynamics simulation protocols for the generation of thin film morphologies. Journal of Chemical Information and Modeling, 63 (1), 2-8. doi: 10.1021/acs.jcim.2c01334
Featured
2018
Journal Article
Automated topology builder version 3.0: prediction of solvation free enthalpies in water and hexane
Stroet, Martin, Caron, Bertrand, Visscher, Koen M., Geerke, Daan P., Malde, Alpeshkumar K. and Mark, Alan E. (2018). Automated topology builder version 3.0: prediction of solvation free enthalpies in water and hexane. Journal of Chemical Theory and Computation, 14 (11) acs.jctc.8b00768, 5834-5845. doi: 10.1021/acs.jctc.8b00768
Featured
2017
Journal Article
Real cost of speed: the effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulations
Reisser, Sabine, Poger, David, Stroet, Martin and Mark, Alan E. (2017). Real cost of speed: the effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulations. Journal of Chemical Theory and Computation, 13 (6), 2367-2372. doi: 10.1021/acs.jctc.7b00178
Featured
2017
Journal Article
Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films
Tonnelé, Claire, Stroet, Martin, Caron, Bertrand, Clulow, Andrew J., Nagiri, Ravi C. R., Malde, Alpeshkumar K., Burn, Paul L., Gentle, Ian R., Mark, Alan E. and Powell, Benjamin J. (2017). Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films. Angewandte Chemie - International Edition, 56 (29), 8402-8406. doi: 10.1002/anie.201610727
Featured
2014
Journal Article
Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies
Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2014). Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies. Journal of Computer-Aided Molecular Design, 28 (3), 221-233. doi: 10.1007/s10822-014-9713-7
Featured
2011
Journal Article
An automated force field topology builder (ATB) and repository: Version 1.0
Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris and Mark, Alan E. (2011). An automated force field topology builder (ATB) and repository: Version 1.0. Journal of Chemical Theory and Computation, 7 (12), 4026-4037. doi: 10.1021/ct200196m
2024
Journal Article
On the Validation of Protein Force Fields Based on Structural Criteria
Stroet, Martin, Setz, Martina, Lee, Thomas, Malde, Alpeshkumar K., van den Bergen, Glen, Sykacek, Peter, Oostenbrink, Chris and Mark, Alan E. (2024). On the Validation of Protein Force Fields Based on Structural Criteria. The Journal of Physical Chemistry B, 128 (19), 4602-4620. doi: 10.1021/acs.jpcb.3c08469
2023
Journal Article
Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisation
Jia, Xinying, Chin, Yanni K.-Y., Zhang, Alan H., Crawford, Theo, Zhu, Yifei, Fletcher, Nicholas L., Zhou, Zihan, Hamilton, Brett R., Stroet, Martin, Thurecht, Kristofer J. and Mobli, Mehdi (2023). Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisation. Communications Chemistry, 6 (1) 48, 1-10. doi: 10.1038/s42004-023-00841-5
2023
Journal Article
Engineering transferable atomic force fields: empirical optimization of hydrocarbon Lennard–Jones interactions by direct mapping of parameter space
Zhou, Zihan, Mark, Alan E. and Stroet, Martin (2023). Engineering transferable atomic force fields: empirical optimization of hydrocarbon Lennard–Jones interactions by direct mapping of parameter space. Journal of Chemical Theory and Computation, 19 (13), 4074-4087. doi: 10.1021/acs.jctc.3c00427
2023
Journal Article
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules
Stroet, Martin, Caron, Bertrand, Engler, Martin S., van der Woning, Jimi, Kauffmann, Aude, van Dijk, Marc, El-Kebir, Mohammed, Visscher, Koen M., Holownia, Josef, Macfarlane, Callum, Bennion, Brian J., Gelpi-Dominguez, Svetlana, Lightstone, Felice C., van der Storm, Tijs, Geerke, Daan P., Mark, Alan E. and Klau, Gunnar W. (2023). OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of Computer-Aided Molecular Design, 37 (8), 357-371. doi: 10.1007/s10822-023-00511-7
2023
Journal Article
Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR
Kuschert, Sarah, Stroet, Martin, Chin, Yanni Ka-Yan, Conibear, Anne Claire, Jia, Xinying, Lee, Thomas, Bartling, Christian Reinhard Otto, Strømgaard, Kristian, Güntert, Peter, Rosengren, Karl Johan, Mark, Alan Edward and Mobli, Mehdi (2023). Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMR. Magnetic Resonance, 4 (1), 57-72. doi: 10.5194/mr-4-57-2023
2022
Other Outputs
Australasian Computational and Simulation Commons (ACSC)
Mark, Alan E. , Stroet, Martin and Nada, Sharif (2022). Australasian Computational and Simulation Commons (ACSC). The University of Queensland. (Collection) doi: 10.48610/62d1f81
2022
Journal Article
Understanding the effect of pH on the solubility and aggregation extent of humic acid in solution by combining simulation and the experiment
Lan, Tu, Wu, Peng, Liu, Ziyi, Stroet, Martin, Liao, Jiali, Chai, Zhifang, Mark, Alan E., Liu, Ning and Wang, Dongqi (2022). Understanding the effect of pH on the solubility and aggregation extent of humic acid in solution by combining simulation and the experiment. Environmental Science and Technology, 56 (2) acs.est.1c05938, 917-927. doi: 10.1021/acs.est.1c05938
2019
Journal Article
Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environment
van den Bergen, Glen, Stroet, Martin, Caron, Bertrand, Poger, David and Mark, Alan E. (2019). Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environment. FEBS Letters, 594 (6) 1873-3468.13705, 1062-1080. doi: 10.1002/1873-3468.13705
2018
Journal Article
Predicting the prevalence of alternative Warfarin tautomers in solution
Malde, Alpeshkumar K., Stroet, Martin, Caron, Bertrand, Visscher, Koen M. and Mark, Alan E. (2018). Predicting the prevalence of alternative Warfarin tautomers in solution. Journal of Chemical Theory and Computation, 14 (8) acs.jctc.8b00453, 4405-4415. doi: 10.1021/acs.jctc.8b00453
2018
Other Outputs
Improving the accuracy of molecular dynamics simulations: parameterisation of interaction potentials for small molecules
Stroet, Martin (2018). Improving the accuracy of molecular dynamics simulations: parameterisation of interaction potentials for small molecules. PhD Thesis, School of Chemistry and Molecular Biosciences, The University of Queensland. doi: 10.14264/uql.2018.432
2017
Journal Article
Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach
Stroet, Martin, Koziara, Katarzyna B, Malde, Alpeshkumar K and Mark, Alan E (2017). Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation Approach. Journal of Chemical Theory and Computation, 13 (12), 6201-6212. doi: 10.1021/acs.jctc.7b00800
2017
Journal Article
The Molecular Origin of Anisotropic Emission in an Organic Light-Emitting Diode
Lee, Thomas, Caron, Bertrand, Stroet, Martin, Huang, David M., Burn, Paul L. and Mark, Alan E. (2017). The Molecular Origin of Anisotropic Emission in an Organic Light-Emitting Diode. Nano Letters, 17 (10), 6464-6468. doi: 10.1021/acs.nanolett.7b03528
2017
Journal Article
Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films
Tonnelé, Claire, Stroet, Martin, Caron, Bertrand, Clulow, Andrew J., Nagiri, Ravi C. R., Malde, Alpeshkumar K., Burn, Paul L., Gentle, Ian R., Mark, Alan E. and Powell, Benjamin J. (2017). Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode films. Angewandte Chemie, 129 (29), 8522-8526. doi: 10.1002/ange.201610727
2015
Conference Publication
Validation and development of the force field parameters for drug and drug-like molecules
Koziara, Katarzyna B., Stroet, Martin, Malde, Alpeshkumar K. and Mark, Alan E. (2015). Validation and development of the force field parameters for drug and drug-like molecules. Biophysical Society 59th Annual Meeting, Baltimore, United States, February 7-11, 2015. St. Louis, United States: Cell Press. doi: 10.1016/j.bpj.2014.11.869
Funding
Current funding
Supervision
Availability
- Dr Martin Stroet is:
- Available for supervision
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