Book Chapter
Poger, David and Mark, Alan E. (2013). Study of proteins and peptides at interfaces by molecular dynamics simulation techniques. Proteins in solution and at interfaces: methods and applications in biotechnology and materials science. (pp. 291-313) edited by Juan M Ruso and Angel Pineiro. Hoboken NJ, United States: John Wiley & Sons, Inc.. doi: 10.1002/9781118523063.ch14
Journal Articles
John, Torsten, Rampioni, Aldo, Poger, David and Mark, Alan E. (2024). Molecular Insights into the Dynamics of Amyloid Fibril Growth: Elongation and Lateral Assembly of GNNQQNY Protofibrils. ACS Chemical Neuroscience, 15 (4), 716-723. doi: 10.1021/acschemneuro.3c00754
Braet, Filip and Poger, David (2023). Let's have a Chat about Chatbot(s) in (Biological) Microscopy. Journal of Microscopy, 292 (2), 59-63. doi: 10.1111/jmi.13230
Poger, David, Yen, Lisa and Braet, Filip (2023). Big data in contemporary electron microscopy: challenges and opportunities in data transfer, compute and management. Histochemistry and Cell Biology, 160 (3), 169-192. doi: 10.1007/s00418-023-02191-8
Barfoot, Shelley, Poger, David and Mark, Alan E. (2020). Understanding the activated form of a class-I fusion protein: modeling the interaction of the Ebola virus glycoprotein 2 with a lipid bilayer. Biochemistry, 59 (41) acs.biochem.0c00527, 4051-4058. doi: 10.1021/acs.biochem.0c00527
Deplazes, Evelyne, Sarrami, Farzaneh and Poger, David (2020). Effect of H3O+ on the structure and dynamics of water at the interface with phospholipid bilayers. The Journal of Physical Chemistry B, 124 (8) acs.jpcb.9b10169, 1361-1373. doi: 10.1021/acs.jpcb.9b10169
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
Poger, 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
Poger, 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
Deplazes, Evelyne, Poger, David, Cornell, Bruce and Cranfield, Charles G. (2018). The effect of H3O+ on the membrane morphology and hydrogen bonding of a phospholipid bilayer. Biophysical Reviews, 10 (5), 1371-1376. doi: 10.1007/s12551-018-0454-z
Deplazes, Evelyne, Poger, David, Cornell, Bruce and Cranfield, Charles G. (2017). The effect of hydronium ions on the structure of phospholipid membranes. Physical Chemistry Chemical Physics, 20 (1), 357-366. doi: 10.1039/c7cp06776c
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
Corbett, 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
Corbett, Michael S. P., Poger, David and Mark, Alan E. (2016). Revisiting the scissor-like mechanism of activation for the erythropoietin receptor. FEBS Letters, 590 (18), 3083-3088. doi: 10.1002/1873-3468.12340
Poger, David, Caron, Bertrand and Mark, Alan E. (2016). Validating lipid force fields against experimental data: progress, challenges and perspectives.. Biochimica et Biophysica Acta, 1858 (7), 1556-1565. doi: 10.1016/j.bbamem.2016.01.029
Poger, David and Mark, Alan E. (2015). Effect of Ring Size in ω-Alicyclic Fatty Acids on the Structural and Dynamical Properties Associated with Fluidity in Lipid Bilayers. Langmuir, 31 (42), 11574-11582. doi: 10.1021/acs.langmuir.5b02635
Poger, David and Mark, Alan E. (2015). A ring to rule them all: the effect of cyclopropane fatty acids on the fluidity of lipid bilayers. Journal of Physical Chemistry B, 119 (17), 5487-5495. doi: 10.1021/acs.jpcb.5b00958
Poger, David, Caron, Bertrand and Mark, Alan E. (2014). Effect of methyl-branched fatty acids on the structure of lipid bilayers. Journal of Physical Chemistry B, 118 (48), 13838-13848. doi: 10.1021/jp503910r
Caron, Bertrand, Mark, Alan E. and Poger, David (2014). Some like it hot: the effect of sterols and hopanoids on lipid ordering at high temperature. Journal of Physical Chemistry Letters, 5 (22), 3953-3957. doi: 10.1021/jz5020778
Poger, David and Mark, Alan E. (2014). Activation of the epidermal growth factor receptor: a series of twists and turns. Biochemistry, 53 (16), 2710-2721. doi: 10.1021/bi401632z
Xue, Ying, He, Lizhong, Middelberg, Anton P. J., Mark, Alan E. and Poger, David (2014). Determining the structure of interfacial peptide films: comparing neutron reflectometry and molecular dynamics simulations. Langmuir, 30 (33), 10080-10089. doi: 10.1021/la501715h
Poger, David and Mark, Alan E. (2013). The relative effect of sterols and hopanoids on lipid bilayers: when comparable is not identical. Journal of Physical Chemistry B, 117 (50), 16129-16140. doi: 10.1021/jp409748d
Poger, David and Mark, Alan E. (2012). Lipid bilayers: the effect of force field on ordering and dynamics. Journal of Chemical Theory and Computation, 8 (11), 4807-4817. doi: 10.1021/ct300675z
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
Chen, Rong, Poger, David and Mark, Alan (2011). Effect of high pressure on fully hydrated DPPC and POPC bilayers. The Journal of Physical Chemistry B, 115 (5), 1038-1044. doi: 10.1021/jp110002q
Groothuizen, Flora S., Poger, David and Mark, Alan E. (2010). Activating the prolactin receptor: Effect of the ligand on the conformation of the extracellular domain. Journal of Chemical Theory and Computation, 6 (10), 3274-3283. doi: 10.1021/ct1003934
Poger, David, van Gunsteren, Wilfred F. and Mark, Alan E. (2010). A new force field for simulating phosphatidylcholine bilayers. Journal of Computational Chemistry, 31 (6), 1117-1125. doi: 10.1002/jcc.21396
Poger, David and Mark, Alan E. (2010). Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation. Proteins: Structure, Function & Bioinformatics, 78 (5), 1163-1174. doi: 10.1002/prot.22636
Poger, David and Mark, Alan E. (2010). On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experiment. Journal of Chemical Theory and Computation, 6 (1), 325-336. doi: 10.1021/ct900487a
Poger, David, Fillaux, Clara, Miras, Roger, Crouzy, Serge, Delangle, Pascale, Mintz, Elisabeth, Den Auwer, Christophe and Ferrand, Michel (2008). Interplay between glutathione, Atx1 and copper: X-ray absorption spectroscopy determination of Cu(I) environment in an Atx1 dimer. Journal of Biological Inorganic Chemistry, 13 (8), 1239-1248. doi: 10.1007/s00775-008-0408-1
Fuchs, Jean-Francois, Nedev, Hristo, Poger, David, Ferrand, Michel, Brenner, Valérie, Dognon, Jean-Pierre and Crouzy, Serge (2006). New model potentials for sulfur-copper(I) and sulfur-mercury(II) interactions in proteins: From ab initio to molecular dynamics. Journal of Computational Chemistry, 27 (7), 837-856. doi: 10.1002/jcc.20392
Poger, David, Fuchs, Jean-Francois, Nedev, Hristo, Ferrand, Michel and Crouzy, Serge (2005). Molecular dynamics study of the metallochaperone Hah1 in its apo and Cu(I)-loaded states: Role of the conserved residue M10. Febs Letters, 579 (24), 5287-5292. doi: 10.1016/j.febslet.2005.08.052
Conference Paper
Corbett, Michael, Poger, David and Mark, Alan E. (2016). A cytokine receptor revolution: activation of the Type-I Cytokine Receptors via protomer rotation. 60th Annual Meeting of the Biophysical Society, Los Angeles, CA, United States, 27 February- 2 March 2016. St. Louis, MO, United States: Cell Press. doi: 10.1016/j.bpj.2015.11.3161