Dr Martin Stroet
Research Fellow
School of Chemistry and Molecular Biosciences
Journal Articles
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Conference Papers
Koziara, K. B., Stroet, M., Malde, A. K. and Mark, A. E. (2015). Validation and development of force field parameters for drug and drug-like molecules. 10th European Biophysical Societies Association (EBSA) European Biophysics Congress, Dresden, Germany, 18-22 July, 2015. New York, NY, United States: Springer.
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
Cao, Yongyin, Stilgoe, Alexander B., Stroet, Martin, Loke, Vincent L. Y., Chen, Lixue, Nieminen, Timo A. and Rubinsztein-Dunlop, Halina (2012). Computational modelling of optical tweezers with many degrees of freedom using dynamic simulation: cylinders, nanowires, and multiple particles. Conference on Optical Trapping and Optical Micromanipulation IX, San Diego, United States, 12-16 August 2012. Bellingham, WA, United States: S P I E - International Society for Optical Engineering. doi: 10.1117/12.930137
Data Collection
Mark, Alan E. , Stroet, Martin and Nada, Sharif (2022). Australasian Computational and Simulation Commons (ACSC). The University of Queensland. (Collection) doi: 10.48610/62d1f81
Thesis
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