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2022 Journal Article PyThinFilm: Automated molecular dynamics simulation protocols for the generation of thin film morphologiesStroet, 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 |
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2018 Journal Article Automated topology builder version 3.0: prediction of solvation free enthalpies in water and hexaneStroet, 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 |
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2017 Journal Article Real cost of speed: the effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulationsReisser, 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 |
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2017 Journal Article Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode filmsTonnelé, 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 |
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2014 Journal Article Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpiesKoziara, 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 |
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2011 Journal Article An automated force field topology builder (ATB) and repository: Version 1.0Malde, 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 |
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2024 Journal Article On the Validation of Protein Force Fields Based on Structural CriteriaStroet, 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 |
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2023 Journal Article Self-cyclisation as a general and efficient platform for peptide and protein macrocyclisationJia, 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 |
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2023 Journal Article Engineering transferable atomic force fields: empirical optimization of hydrocarbon Lennard–Jones interactions by direct mapping of parameter spaceZhou, 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 |
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2023 Journal Article OFraMP: a fragment-based tool to facilitate the parametrization of large moleculesStroet, 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 |
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2023 Journal Article Facilitating the structural characterisation of non-canonical amino acids in biomolecular NMRKuschert, 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 |
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2022 Journal Article Understanding the effect of pH on the solubility and aggregation extent of humic acid in solution by combining simulation and the experimentLan, 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 |
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2019 Journal Article Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environmentvan 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 |
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2018 Journal Article Predicting the prevalence of alternative Warfarin tautomers in solutionMalde, 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 |
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2017 Journal Article Optimization of Empirical Force Fields by Parameter Space Mapping: A Single-Step Perturbation ApproachStroet, 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 |
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2017 Journal Article The Molecular Origin of Anisotropic Emission in an Organic Light-Emitting DiodeLee, 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 |
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2017 Journal Article Elucidating the spatial arrangement of emitter molecules in organic light-emitting diode filmsTonnelé, 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 |
