Publications 2017 - Theoretical Biophysics

A. H. Bahrami, M. G. Lin, X. Ren, J. H. Hurley, G. Hummer, “Scaffolding the cup-shaped double membrane in autophagy,” PLoS Comput Biol13(10): e1005817 (2017). [https://doi.org/10.1371/journal.pcbi.1005817]

A. H. Bahrami, G. Hummer, “Formation and stability of lipid membrane nanotubes,” ACS Nano, 11, 9558-9565 (2017). [https://doi.org/10.1021/acsnano.7b05542]

R. M. Bhaskara, S. Linker, M. Vögele, J. Köfinger, G. Hummer, “Carbon nanotubes mediate fusion of lipid vesicles,” ACS Nano 12, 1273-1280 (2017). [https://dx.doi.org/10.1021/acsnano.6b05434]

E. Chiavazzo, R.R. Coifman, R. Covino, C.W. Gear, A.S. Georgiou, G. Hummer, I.G. Kevrekidis, “Intrinsic Map Dynamics exploration for uncharted effective free energy landscapes,” Proc. Natl. Acad. Sci. U.S.A. 114, E5494–E5503 (2017). [https://doi.org/10.1073/pnas.1621481114]

P. Cossio, D. Rohr, F. Baruffa, M. Rampp, V. Lindenstruth, G. Hummer, “BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images,” Computer Phys. Commun. 210, 163-171 (2017). [https://dx.doi.org/10.1016/j.cpc.2016.09.014]

M. Diskowski, A.R. Mehdipour, D. Wunnicke, D. J. Mills, V. Mikusevic, N. Bärland, J. Hoffmann, N. Morgner, H.J. Steinhoff, G . Hummer, J. Vonck, I. Hänelt, “Helical jackknives control the gates of the double pore K+ uptake system KtrAB”, /eLife/ 6, e24303 (2017). [https://doi.org/10.7554/eLife.24303]

A. Ghysels, R. Venable, R. Pastor, G. Hummer, “Position-dependent diffusion tensors in anisotropic media from simulation: oxygen transport in and through membranes,” J. Chem. Theor. Comput., 13, 2962-2976 (2017). [https://doi.org/10.1021/acs.jctc.7b00039]

K. Halbleib, K. Pesek, R. Covino, H. F. Hofbauer, D. Wunnicke, I. Hänelt, G. Hummer, R. Ernst, “Activation of the unfolded protein response by lipid bilayer stress,” Mol. Cell 67, 63-684 (2017). [https://doi.org/10.1016/j.molcel.2017.06.012]

G. Hummer , A. Szabo, “Dynamics of the orientational factor in fluorescence resonance energy transfer,” J. Phys. Chem. B 121, 3331-3339 (2017) [Klaus Schulten Festschrift] [https://dx.doi.org/10.1021/acs.jpcb.6b08345]

H. Jung, K.-i. Okazaki, G. Hummer, “Transition path sampling of rare events by shooting from the top,” J. Chem. Phys. 147, 152716 (2017). [https://doi.org/10.1063/1.4997378]

C. Karathansis, G. Hummer, M. Heilemann, “Molecule counts in localization microscopy with organic fluorophores,” ChemPhysChem 18, 942-948 (2017). [https://dx.doi.org/10.1002/cphc.201601425]

C. T. Leahy, A. Kells, G. Hummer, E. Rosta, N.V. Buchete, “Peptide dimerization-dissociation rates from replica exchange molecular dynamics,” J. Chem. Phys. 147, 152725 (2017). [https://doi.org/10.1063/1.5004774]

D. Malinverni, A. Jost Lopez, P. De Los Rios, G. Hummer, A. Barducci, “Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis,” eLife, 6, e23471 (2017). [https://doi.org/10.7554/eLife.23471]

L. Martini, A. Kells, R. Covino, G. Hummer, N.V. Buchete, E. Rosta, “Variational identification of Markovian transition states,” Phys. Rev. X 7, 031060 (2017). [https://doi.org/10.1103/PhysRevX.7.031060]

A. Nöll, C. Thomas, V. Herbring, T. Zollmann, K. Barth, A. R. Mehdipour, T. M. Tomasiak, S. Brüchert, B. Joseph, R. Abele, V. Oliéric, M. Wang, K. Diederichs, G. Hummer, R. M. Stroud, K. M. Pos, R. Tampé, “Structure and mechanistic basis of a functional homolog of the antigen transporter TAP,” Proc. Natl. Acad. Sci. U.S.A. 114, E438–E447 (2017). [https://dx.doi.org/10.1073/pnas.1620009114]

K. Reichel, O. Fisette, T. Braun, O.F. Lange, G. Hummer, and L.V. Schäfer, “Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints,”Proteins Struct. Funct. Bioinf. 85, 812-826 (2017). [https://dx.doi.org/10.1002/prot.25224]

M. Simonson, G. Hummer, B. Roux, “On the equivalence of M- and P-summation in calculations of ionic solvation free energies,”J. Phys. Chem. A 121, 1525-1530 (2017). [https://dx.doi.org/10.1021/acs.jpca.6b12691]

L. Stelzl, G. Hummer, “Kinetics from replica exchange molecular dynamics simulations,” J. Chem. Theory. Comput. 13, 3927-3935 (2017). [https://doi.org/10.1021/acs.jctc.7b00372]

L. Stelzl, N. Erlenbach, M. Heinz, T. Prisner, G. Hummer, “Resolving the conformational dynamics of dna with Ångstrom resolution by PELDOR and molecular dynamics,” J. Am. Chem. Soc. [Communication] 139, 11674-11677 (2017). [https://doi.org/10.1021/jacs.7b05363]

 

Master's Theses

Michael Gecht: Biophysical analysis of a membrane sensing amphipathic  helix in vitro and in silico. Goethe-Universität, Frankfurt am Main, 2017 

Kara Grotz: Conformational Dynamics of Single-Stranded Nucleic Acids - A  Comparison of Molecular Dynamics Simulations to Single-Molecule FRET  Experiments. Goethe-Universität, Frankfurt am Main, 2017 

Stephanie Linker: Predicting Drug-Fragment Binding Sites with Molecular  Dynamics Simulations and Markov State Models. Goethe-Universität, Frankfurt am Main, 2017 

Laura Schulz: Lead discovery from the mycobacterial ATP synthase F_O  rotor ring and characterisation of its binding site. Goethe-Universität, Frankfurt am Main, 2017

Contact:

Max Planck Institute of Biophysics

Prof. Dr. Gerhard Hummer, Director
Department of Theoretical Biophysics
Secretary: Christina Brandt

Phone: +49 (0) 69 6303-2501
E-mail: office-hummer(at)biophys.mpg.de

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