Molecular Dynamics

Organisational unit: Research Group

  1. 2017
  2. Tose, L. V., Santos, N. A., Rodrigues, R. R. T., Murgu, M., Gomes, A. F., Vasconcelos, G. A., ... Romão, W. (2017). Isomeric separation of cannabinoids by UPLC combined with ionic mobility mass spectrometry (TWIM-MS)-Part I. International Journal of Mass Spectrometry, 418, 112-121. DOI: 10.1016/j.ijms.2016.10.018
  3. Souza, P. C. T., Textor, L. C., Melo, D. C., Nascimento, A. S., Skaf, M. S., & Polikarpov, I. (2017). An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position. Scientific Reports, 7(1), 1-11. [3509]. DOI: 10.1038/s41598-017-03774-x
  4. Lampel, A., McPhee, S. A., Park, H-A., Scott, G. K., Humagain, S., Hekstra, D. R., ... Ulijn, R. V. (2017). Polymeric peptide pigments with sequence-encoded properties. Science, 356(6342), 1064-1068. DOI: 10.1126/science.aal5005
  5. Venable, R. M., Ingólfsson, H. I., Lerner, M. G., Perrin, B. S., Camley, B. A., Marrink, S. J., ... Pastor, R. W. (2017). Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions. The Journal of Physical Chemistry B, 121(15), 3443–3457. [jpcb.6b09111]. DOI: 10.1021/acs.jpcb.6b09111
  6. Kanduc, M., Schlaich, A., de Vries, A. H., Jouhet, J., Marechal, E., Deme, B., ... Schneck, E. (2017). Tight cohesion between glycolipid membranes results from balanced water-headgroup interactions. Nature Communications, 8, [14899]. DOI: 10.1038/ncomms14899
  7. Melo, M. N., Arnarez, C., Sikkema, H., Kumar, N., Walko, M., Berendsen, H. J. C., ... Ingólfsson, H. I. (2017). High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating. Journal of the American Chemical Society, 139(7), 2664-2671. DOI: 10.1021/jacs.6b11091
  8. Arnarez, C., & Marrink, S. J. (2017). Chapter 1: Computational Microscopy of Mitochondrial Membranes. In K. Kholmurodov (Ed.), Computer Design for New Drugs and Materials: Molecular Dynamics of Nanoscale Phenomena (pp. 1). Nova Science Publishers.
  9. Swier, L. J. Y. M., Monjas, L., Reeßing, F., Oudshoorn, R. C., Aisyah, A., Primke, T., ... Slotboom, D. J. (2017). Insight into the complete substrate-binding pocket of ThiT by chemical and genetic mutations. MedChemCommun, 8(5), 1121-1130. DOI: 10.1039/C7MD00079K
  10. Maingi, V., Burns, J. R., Uusitalo, J. J., Howorka, S., Marrink, S. J., & Sansom, M. S. P. (2017). Stability and dynamics of membrane-spanning DNA nanopores. Nature Communications, 8, 1-12. [14784]. DOI: 10.1038/ncomms14784
  11. Su, J. (2017). The simulation studies of the interplay of peptides with lipids [Groningen]: University of Groningen
  12. 2016
  13. Smeets, C. J. L. M., Zmorzynska, J., Melo, M. N., Stargardt, A., Dooley, C., Bakalkin, G., ... Verbeek, D. S. (2016). Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23. Human Molecular Genetics, 25(13), 2728-2737. DOI: 10.1093/hmg/ddw130
  14. Ingólfsson, H. I., Arnarez, C., Periole, X., & Marrink, S. J. (2016). Computational 'microscopy' of cellular membranes. Journal of Cell Science, 129(2), 257-268. DOI: 10.1242/jcs.176040
  15. Antillón, A., De Vries, A. H., Espinosa-caballero, M., Falcón-gonzález, J. M., Flores Romero, D., González–damián, J., ... Johnson, C. J. (Ed.) (2016). An Amphotericin B Derivative Equally Potent to Amphotericin B and with Increased Safety. PLoS ONE, 11(9), 1-38. [e0162171]. DOI: 10.1371/journal.pone.0162171
  16. Uusitalo, J. J. (2016). Covering all the bases: Coarse-grained model design and application for nucleic acids [Groningen]: University of Groningen
  17. Paulechka, E., Wassenaar, T., Kroenlein, K., Kazakov, A., & Smolyanitsky, A. (2016). Nucleobase-functionalized grapheme nanoribbons for accurate high-speed DNA sequencing. Nanoscale, 8, 1861-1867. DOI: 10.1039/C5NR07061A
  18. 2015
  19. Uytterhoeven, V., Lauwers, E., Maes, I., Miskiewicz, K., Melo, M., Swerts, J., ... Verstreken, P. (2015). Hsc70-4 Deforms Membranes to Promote Synaptic Protein Turnover by Endosomal Microautophagy. Neuron, 88(4), 735-748. DOI: 10.1016/j.neuron.2015.10.012
  20. Uusitalo, J. J., Ingolfsson, H. I., Akhshi, P., Tieleman, D. P., & Marrink, S. J. (2015). Martini Coarse-Grained Force Field: Extension to DNA. Journal of Chemical Theory and Computation, 11(8), 3932-3945. DOI: 10.1021/acs.jctc.5b00286
  21. Oktaviani, N. A., Risor, M. W., Lee, Y-H., Megens, R. P., de Jong, D. H., Otten, R., ... Mulder, F. A. A. (2015). Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. Journal of Biomolecular Nmr, 62(2), 129-142. DOI: 10.1007/s10858-015-9925-8
  22. Barrera Guisasola, E. E., Andujar, S. A., Hubin, E., Broersen, K., Kraan, I. M., Mendez, L., ... Enriz, R. D. (2015). New mimetic peptides inhibitors of A beta aggregation. Molecular guidance for rational drug design. European Journal of Medicinal Chemistry, 95, 136-152. DOI: 10.1016/j.ejmech.2015.03.042
  23. Lopez, C. A., Bellesia, G., Redondo, A., Langan, P., Chundawat, S. P. S., Dale, B. E., ... Gnanakaran, S. (2015). MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers. The Journal of Physical Chemistry B, 119(2), 465-473. DOI: 10.1021/jp5105938
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