Professur für Computational Biology

Address:
Staudtstraße 5
91058 Erlangen


Related Project(s)


(SFB1027: Physical modeling of non-equilibrium processes in biological systems (Saarland University)):
SFB1027: Cooperative Action of SNARE Peptides in Fusion
Prof. Dr. Rainer Böckmann
(01/01/2017 - 31/12/2020)


GRK 1962: Dynamische Wechselwirkungen an Biologischen Membranen – von Einzelmolekülen zum Gewebe
Prof. Dr. Rainer Böckmann
(01/04/2014 - 30/09/2018)


The role of SNARE TMDs during exocytosis of secretory granules
Prof. Dr. Rainer Böckmann
(01/06/2009 - 30/06/2012)



Publications (Download BibTeX)

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Sandoval, A., Eichler, S., Madathil, S., Reeves, P.J., Fahmy, K., & Böckmann, R. (2016). The Molecular Switching Mechanism at the Conserved D(E)RY Motif in Class-A GPCRs. Biophysical Journal, 111(1), 79-89. https://dx.doi.org/10.1016/j.bpj.2016.06.004
Dhara, M., Yarzagaray, A., Makke, M., Schindeldecker, B., Schwarz, Y., Shaaban, A.,... Bruns, D. (2016). v-SNARE transmembrane domains function as catalysts for vesicle fusion. eLife, 5. https://dx.doi.org/10.7554/eLife.17571
Han, J., Pluhackova, K., & Böckmann, R. (2016). Exploring the Formation and the Structure of Synaptobrevin Oligomers in a Model Membrane. Biophysical Journal, 110(9), 2004-15. https://dx.doi.org/10.1016/j.bpj.2016.04.006
Han, J., Pluhackova, K., Bruns, D., & Böckmann, R. (2016). Synaptobrevin transmembrane domain determines the structure and dynamics of the SNARE motif and the linker region. BBA - Biochimica et Biophysica Acta, 1858(4), 855-65. https://dx.doi.org/10.1016/j.bbamem.2016.01.030
Pluhackova, K., Kirsch, S., Han, J., Sun, L., Jiang, Z., Unruh, T., & Böckmann, R. (2016). A Critical Comparison of Biomembrane Force Fields: Structure and Dynamics of Model DMPC, POPC, and POPE Bilayers. Journal of Physical Chemistry B, 120(16), 3888-903. https://dx.doi.org/10.1021/acs.jpcb.6b01870
Bertelshofer, F., Sun, L., Greiner, G., & Böckmann, R. (2015). GroPBS: Fast Solver for Implicit Electrostatics of Biomolecules. Frontiers in Bioengineering and Biotechnology, 3, 186. https://dx.doi.org/10.3389/fbioe.2015.00186
Pluhackova, K., Morhenn, H., Lautner, L., Lohstroh, W., Nemkovski, K., Unruh, T., & Böckmann, R. (2015). Extension of the LOPLS-AA Force Field for Alcohols, Esters, and Monoolein Bilayers and its Validation by Neutron Scattering Experiments. Journal of Physical Chemistry B, 119(49), 15287-99. https://dx.doi.org/10.1021/acs.jpcb.5b08569
Jiang, Z., Zhang, H., & Böckmann, R. (2015). Allostery in BAX Protein Activation. Journal of biomolecular structure & dynamics, 1-29. https://dx.doi.org/10.1080/07391102.2015.1119731
Pluhackova, K., Wassenaar, T., Kirsch, S., & Böckmann, R. (2015). Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer. Journal of Physical Chemistry B, 119(12), 4396-408. https://dx.doi.org/10.1021/acs.jpcb.5b00434
Han, J., Pluhackova, K., Wassenaar, T., & Böckmann, R. (2015). Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations. Biophysical Journal, 109(4), 760-771. https://dx.doi.org/10.1016/j.bpj.2015.06.049
Pluhackova, K., & Böckmann, R. (2015). Biomembranes in atomistic and coarse-grained simulations. Journal of Physics: Condensed Matter, 27(32). https://dx.doi.org/10.1088/0953-8984/27/32/323103
Wassenaar, T., Ingolfsson, H., Böckmann, R., Tieleman, P., & Marrink, S.-J. (2015). Computational lipidomics with insane: A versatile tool for generating custom membranes for molecular simulations. Journal of Chemical Theory and Computation, 11(5), 2144-2155. https://dx.doi.org/10.1021/acs.jctc.5b00209
Kociurzynski, R., Pannuzzo, M., & Böckmann, R. (2015). Phase Transition of Glycolipid Membranes Studied by Coarse-Grained Simulations. Langmuir, 31(34), 9379-9387. https://dx.doi.org/10.1021/acs.langmuir.5b01617
Wassenaar, T., Pluhackova, K., Moussatova, A., Sengupta, D., Marrink, S.-J., Tieleman, P., & Böckmann, R. (2015). High-throughput simulations of dimer and trimer assembly of membrane proteins. The DAFT approach. Journal of Chemical Theory and Computation, 11(5), 2278-2291. https://dx.doi.org/10.1021/ct5010092
Pannuzzo, M., Raudino, A., & Böckmann, R. (2014). Peptide-induced membrane curvature in edge-stabilized open bilayers: a theoretical and molecular dynamics study. Journal of Chemical Physics, 141(2), 024901. https://dx.doi.org/10.1063/1.4885340
Pannuzzo, M., & Böckmann, R. (2014). Energetic view on membrane pore formation. Biophysical Journal, 106(1), 1-2. https://dx.doi.org/10.1016/j.bpj.2013.12.001
Sorrentino, R., Böckmann, R., & Fiorillo, M.T. (2014). HLA-B27 and antigen presentation: At the crossroads between immune defense and autoimmunity. Molecular Immunology, 57(1), 22-27. https://dx.doi.org/10.1016/j.molimm.2013.06.017
Wassenaar, T., Pluhackova, K., Böckmann, R., Marrink, S.-J., & Tieleman, P. (2014). Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models. Journal of Chemical Theory and Computation, 10(2), 676-690. https://dx.doi.org/10.1021/ct400617g
Pluhackova, K., Wassenaar, T., & Böckmann, R. (2013). Molecular dynamics simulations of membrane proteins. Methods in molecular biology (Clifton, N.J.), 1033, 85-101. https://dx.doi.org/10.1007/978-1-62703-487-6_6
Nurzia, E., Narzi, D., Cauli, A., Mathieu, A., Tedeschi, V., Caristi, S.,... Fiorillo, M.T. (2012). Interaction pattern of Arg 62 in the A-pocket of differentially disease-associated HLA-B27 subtypes suggests distinct TCR binding modes. PLoS ONE, 7(3), e32865. https://dx.doi.org/10.1371/journal.pone.0032865


Publications in addition (Download BibTeX)


Kirsch, S., Kugemann, A., Carpaneto, A., Böckmann, R., & Dietrich, P. (2018). Phosphatidylinositol-3,5-bisphosphate lipid-binding-induced activation of the human two-pore channel 2. Cellular and Molecular Life Sciences. https://dx.doi.org/10.1007/s00018-018-2829-5
Ilyaskin, A., Kirsch, S., Böckmann, R., Sticht, H., Korbmacher, C., Härteis, S., & Diakov, A. (2018). The degenerin region of the human bile acid-sensitive ion channel (BASIC) is involved in channel inhibition by calcium and activation by bile acids. Pflugers Archiv : European journal of physiology. https://dx.doi.org/10.1007/s00424-018-2142-z
Sun, L., & Böckmann, R. (2017). Membrane phase transition during heating and cooling: molecular insight into reversible melting. European biophysics journal : EBJ. https://dx.doi.org/10.1007/s00249-017-1237-3

Last updated on 2019-24-04 at 10:26