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2019 Journal Article Effect of triclosan and chloroxylenol on bacterial membranesPoger, David and Mark, Alan E. (2019). Effect of triclosan and chloroxylenol on bacterial membranes. The Journal of Physical Chemistry B, 123 (25) acs.jpcb.9b02588, 5291-5301. doi: 10.1021/acs.jpcb.9b02588 |
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2019 Journal Article Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approachEngler, Martin S., Caron, Bertrand, Veen, Lourens, Geerke, Daan P., Mark, Alan E. and Klau, Gunnar W. (2019). Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms for Molecular Biology, 14 (1) 1, 1. doi: 10.1186/s13015-019-0138-7 |
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2019 Journal Article Probing the pharmacological binding sites of P-glycoprotein using umbrella sampling simulationsSubramanian, Nandhitha, Schumann-Gillett, Alexandra, Mark, Alan E. and O’Mara, Megan L. (2019). Probing the pharmacological binding sites of P-glycoprotein using umbrella sampling simulations. Journal of Chemical Information and Modeling, 59 (5) acs.jcim.8b00624, 2287-2298. doi: 10.1021/acs.jcim.8b00624 |
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2018 Journal Article Could cardiolipin protect membranes against the action of certain antimicrobial peptides?: Aurein 1.2, a Case StudyPoger, David, Pöyry, Sanja and Mark, Alan E. (2018). Could cardiolipin protect membranes against the action of certain antimicrobial peptides?: Aurein 1.2, a Case Study. ACS Omega, 3 (12), 16453-16464. doi: 10.1021/acsomega.8b02710 |
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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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2018 Journal Article Morphology of a bulk heterojunction photovoltaic cell with low donor concentrationLee, Thomas, Sanzogni, Audrey, Zhangzhou, Ningxin, Burn, Paul L. and Mark, Alan E. (2018). Morphology of a bulk heterojunction photovoltaic cell with low donor concentration. ACS Applied Materials and Interfaces, 10 (38) acsami.8b10321, 32413-32419. doi: 10.1021/acsami.8b10321 |
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2018 Conference Publication Understanding how antimicrobial peptides interact with membranesvan den Bergen, Glen and Mark, Alan (2018). Understanding how antimicrobial peptides interact with membranes. HOBOKEN: WILEY. |
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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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2018 Journal Article Effect of Binding on Enantioselectivity of Epoxide HydrolaseZaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018). Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 (3), 630-640. doi: 10.1021/acs.jcim.7b00353 |
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2018 Journal Article The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environmentCondic-Jurkic, Karmen, Subramanian, Nandhitha, Mark, Alan E. and O'Mara, Megan L. (2018). The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment. PloS One, 13 (1) e0191882, 1-24. doi: 10.1371/journal.pone.0191882 |
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2018 Journal Article Developments in Glycopeptide AntibioticsBlaskovich, Mark A. T., Hansford, Karl A., Butler, Mark S., Jia, ZhiGuang, Mark, Alan E. and Cooper, Matthew A. (2018). Developments in Glycopeptide Antibiotics. ACS Infectious Diseases, 4 (5), 715-735. doi: 10.1021/acsinfecdis.7b00258 |
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2018 Journal Article Validation of molecular simulation: an overview of issuesvan Gunsteren, Wilfred F., Daura, Xavier, Hansen, Niels, Mark, Alan E., Oostenbrink, Chris, Riniker, Sereina and Smith, Lorna J. (2018). Validation of molecular simulation: an overview of issues. Angewandte Chemie - International Edition, 57 (4), 884-902. doi: 10.1002/anie.201702945 |
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2018 Conference Publication The use of peptide-membrane interactions in the design of selective and potent sodium channel inhibitorsSchroeder, Christina, Agwa, Akello, Mueller, Alexander, Chow, Chun Yuen, Peigneur, Steve, Lawrence, Nicole, Deplazes, Evelyne, Mark, Alan, Craik, David, Tytgat, Jan, King, Glenn, Vetter, Irina and Henriques, Sonia Troeira (2018). The use of peptide-membrane interactions in the design of selective and potent sodium channel inhibitors. 35th European Peptide Symposium, Dublin City University, Ireland, 26-31 August 2018. Oxford, United Kingdom: John Wiley & Sons. |
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2018 Conference Publication Multiple-choice knapsack for assigning partial atomic charges in drug-like moleculesEngler, Martin S., Caron, Bertrand, Veen, Lourens, Geerke, Daan P., Mark, Alan E. and Klau, Gunnar W. (2018). Multiple-choice knapsack for assigning partial atomic charges in drug-like molecules. 18th International Workshop on Algorithms in Bioinformatics (WABI 2018), Helsinki, Finland, 20-22 August 2018. Wadern, Germany: Schloss Dagstuhl. doi: 10.4230/LIPIcs.WABI.2018.16 |
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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 A potential new, stable state of the E-cadherin strand-swapped dimer in solutionSchumann-Gillett, Alexandra, Mark, Alan E., Deplazes, Evelyne and O'Mara, Megan L. (2017). A potential new, stable state of the E-cadherin strand-swapped dimer in solution. European Biophysics Journal, 47 (1), 59-67. doi: 10.1007/s00249-017-1229-3 |
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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 Do all X-ray structures of protein-ligand complexes represent functional states? EPOR, a case studyCorbett, Michael S. P., Mark, Alan E. and Poger, David (2017). Do all X-ray structures of protein-ligand complexes represent functional states? EPOR, a case study. Biophysical Journal, 112 (4), 595-604. doi: 10.1016/j.bpj.2016.12.042 |
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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 |
