Dr Astrid Brandner

Astrid

Research

Parameterisation of coarse-grained models for a range of biomolecules and simulation of large-scale bacterial cell envelope simulations.

Publication list

  • Brandner AF, Smith IPS, Marrink SJ, Souza PCT, Khalid S. (2025), "Systematic Approach to Parametrization of Disaccharides for the Martini 3 Coarse-Grained Force Field". JCIM,  DOI: 10.1021/acs.jcim.4c01874
  • Brandner AF, Prakaash D, Blanco González A, Waterhouse F, Khalid S, (2024), Faster but Not Sweeter: A Model of the Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 version with Accelerated Kinetics, JCTC,  DOI: 10.1021/acs.jctc.4c00374
  • van den Berg B, Silale A, Basle A, Bradner A F, Mader S, Khalid, S, (2022), "Structural basis for host recognition and superinfection exclusion by bacteriophage T5", Proc. Natl. Acad. Sci. USA, https://doi.org/10.1073/pnas.2211672119
  • Bochicchio A, Brandner AF, Engberg O, Huster D, Böckmann RA. (2020) “Spontaneous membrane nanodomain formation in the absence or presence of the neurotransmitter serotonin.” Front. Cell Dev. Biol., 8, 601145. https://doi.org/10.3389/fcell.2020.601145
  • Engberg O, Bochicchio A, Brandner AF, Gupta A, Dey Simli, Böckmann RA, Maiti S, Huster D. (2020) “Serotonin alters the phase equilibrium of a ternary mixture of phospholipids and cholesterol.” Front. Physiol., 11, 578868. https://doi.org/10.3389/fphys.2020.578868
  • Brandner AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F. (2019) “Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics.” Sci Rep, 9, 16450. https://doi.org/10.1038/s41598-019-52760-y
  • Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A. (2019) “Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking.” Mitochondrion, 49, 234-244. https://doi.org/10.1016/j.mito.2019.06.010
  • De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A. (2019) “A molecular perspective on mitochondrial membrane fusion: from the key players to oligomerization and tethering of mitofusin.” J. Membr. Biol., 252(4), 293-306. https://doi.org/10.1007/s00232-019-00089-y
  • Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A. (2019) “Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.”  Data in brief, 26, 104460. https://doi.org/10.1016/j.dib.2019.104460
  • Brandner, AF, Timr S, Melchionna S, Derreumaux P, Baaden M, Sterpone F. (2019) “Advancing Multi-Scale Simulation Methods for Biological Membrane Systems.” Biophys. J., 116(3), 373a-374a. https://doi.org/10.1016/j.bpj.2018.11.2031
  • Brandner A, Schüller A, Melo F, Pantano S. (2018) “Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes.” Biochem. Biophys. Res. Commun., 498(2), 319-326. https://doi.org/10.1016/j.bbrc.2017.09.086
  • Darré L, Machado MR, Brandner AF, González HC, Ferreira S, Pantano S. (2015) “SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics.” J. Chem. Theory Comput., 11(2), 723-739. https://doi.org/10.1021/ct5007746
  • Dans PD, Darré L, Machado MR, Zeida A, Brandner AF, Pantano S. (2013) “Assessing the accuracy of the SIRAH force field to model DNA at coarse grain level.” In Adv. Bioinform. (eds Setubal JC, Almeida NF), 71-81. https://doi.org/10.1007/978-3-319-02624-4_7

 

Contact details
Department of Biochemistry,
University of Oxford,
South Parks Road
Oxford
OX1 3QU
U.K.

E-mail: astrid.brandner@bioch.ox.ac.uk