The University of Queensland

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Validation and development of force field parameters for drug and drug-like molecules

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.

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

Computational modelling of optical tweezers with many degrees of freedom using dynamic simulation: cylinders, nanowires, and multiple particles

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

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

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