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2011
  1. Van den Bogaart G, Meyenberg K, Risselada HJ, Amin H, Willig KI, Hubrich BE, Dier M, Hell SW, Grubmüller H, Diederichsen U, Jahn R. Membrane protein sequestering by ionic protein-lipid Interactions. Nature 479: 552-55 (2011) [pdf]
  2. Buelens FP, Grubmüller H. Linear-scaling soft-core scheme for alchemical free energy calculations. J. Comp. Chem. 33: 25-33 (2011) [pdf]
  3. Kutzner C, Grubmüller H, de Groot BL, Zachariae U. Computational Electrophysiology: The Molecular Dynamics of Ion Channel Permeation and Selectivity in Atomistic Detail. Biophys J. 101: 809-817 (2011) [pdf] [New&Notable]
  4. Hoefling M, Lima N, Haenni D, Seidel CAM, Schuler B, Grubmüller H. Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach. PLOS ONE 6: e19791 (2011) [pdf]
  5. Donnini S, Tegeler F, Groenhof G, Grubmüller H. Constant pH Molecular Dynamics in Explicit Solvent with lambda-Dynamics. J. Chem Theory and Comp 7: 1962-1978 (2011) [pdf]
  6. Risselada HJ, Marrink SJ, Müller M. Curvature-dependent elastic properties of liquid-ordered domains result in inverted domain sorting on uni-axially compressed vesicles. Phys. Rev. Lett. 106: 148102 (2011) [pdf]
  7. Hub JS, de Groot BL. Comment on Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory. J. Phys. Chem. B 115: 8364–8366 (2011) [pdf]
  8. Boukharta L, Keranen H, Stary-Weinzinger A, Wallin G, de Groot BL, Åqvist J. Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers. Biochem. 50: 6146–6156 (2011) [pdf]
  9. Boggio-Pasqua M, Groenhof G. Controlling the photochemistry of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. J. Phys.Chem. 115: 7021-7028 (2011) [pdf]
  10. Van den Bogaart G, Thutupalli S, Risselada HJ, Holt M, Riedel D, Herminghaus S, Grubmüller H, Jahn R. Synaptotagmin-1: a distance regulator acting upstream of SNARE nucleation? Nat. Struct. Mol. Biol. 18: 805-812 (2011) [pdf]
  11. Seeliger D, Buelens FP, Goette M, de Groot BL, and Grubmüller H. Towards computional specificity screening of DNA-binding proteins. Nucl.Acids Res. July: 1–10 (2011) [pdf]
  12. Kutzner C, Czub J, and Grubmüller H. Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS. J. Chem Theory and Comp. 7: 1381-1393 (2011) [pdf]
  13. Czub J and Grubmüller H. Torsional elasticity and energetics of F1-ATPase. PNAS 108; 7408-7413 (2011) [pdf]
  14. Kappel C, Grubmüller H. Velocity dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophys. J. 100: 1109-1119 (2011) [pdf]
  15. Risselada HJ, Kutzner C, Grubmüller H. Caught in the act: Visualization of SNARE-mediated fusion events in molecular detail. Chembiochem 12: 1049-1055 (2011) [pdf]
  16. de Jong DH, Schäfer LV, de Vries AH, Marrink SJ, Berendsen HJC, and Grubmüller H. Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations. J. Comput. Chem. 32: 1919-1928 (2011) [pdf]
  17. Matthes D, Gapsys V, Daebel V, and de Groot BL. Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization. PLoS ONE 6: e19129 (2011) [pdf]
  18. de Groot BL and Hub JS. A Decade of Debate: Significance of CO2 Permeation through Membrane Channels still Controversial. ChemPhysChem 12: 1021-1022 (2011) [pdf]


2010
  1. Villinger S, Briones R, Giller K, Zachariae U, Lange A, de Groot BL, Griesinger C, Becker S, and Zweckstetter M. Functional dynamics in the voltage dependent anion channel. Proc. Nat. Acad. Sci. 107: 22546-22551 (2010) [pdf]
  2. Hub JS, Aponte-Santamaria C, Grubmüller H, and de Groot BL. Voltage-Regulated Water Flux through Aquaporin Channels in Silico. Biophys. Journal 99: L97-L99 (2010) [pdf]
  3. Hub JS, de Groot BL, and van der Spoel D. g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates. JCTC 6: 3713-3720 (2010) [pdf]
  4. Lopez Cascales JJ, Oliviera Costa SD, de Groot BL, and Walters DE. Binding of Glutamate to the Umami Receptor. Biophys. Chem. 152: 139-144 (2010) [pdf]
  5. Hub JS, Winkler F, Merrick M, and de Groot BL. Potentials of mean force and permeabilities for carbon dioxide, ammonia, and water flux across a Rhesus protein channel and lipid membranes. J. Am. Chem. Soc. 132: 13251-13263 (2010) [pdf]
  6. Bock J, Hutchings B, Grubmüller H, Woodbury DJ. Chemomechanical Regulation of SNARE proteins studied with Molecular Dynamics Simulations. Biophys. J. 99: 1221-1230 (2010) [pdf]
  7. Aponte C, Hub JS, and de Groot BL. Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin. PCCP 12: 10246-10254 (2010) [pdf]
  8. Kappel C, Zachariae U, Dölker N, and Grubmüller H. An Unusual Hydrophobic Core Confers Extreme Flexibility to HEAT Repeat Proteins. Biophys. J. 99: 1596-1603 (2010) [pdf]
  9. Forwood JK, Lange A, Zachariae U, Marfori M, Preast C, Grubmüller H, Stewart M, Corbett AH, and Kobe B. Quantitative Structural Analysis of Importin-b Flexibility: Paradigm for Solenoid Protein Structures. Structure 18: 1171-1183 (2010) [pdf]
  10. Woehri A, Katona G, Johansson LC, Fritz E, Malmerberg E, Andersson M, Vincent J, Eklund M, Cammarata M, Wulff M, Davidsson J, Groenhof G, and Neutze R. Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction. Science 328: 630-633 (2010) [pdf]
  11. Lange OF, van der Spoel D, and de Groot BL. Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data. Biophys. J. 99: 647-655 (2010) [pdf]
  12. Nunes JM, Hensen U, Ge L, Lipinsky M, Helenius J, Grubmüller H, and Müller DJA. “Force Buffer” Protecting Immunoglobin Titin. Angewandte Chemie-International. 49: 3528-3531 (2010) [pdf]
  13. Wolf MG, Hoefling M, Aponte-Santamaria C, Grubmüller H, and Groenhof G. g_membed: Efficient insertion of a membrane protein into an equilibriated lipid bilayer with minimal perturbation. J. Comp.Chem. 31: 2169-2174 (2010) [pdf]
  14. Hub JS, Kubitzki M, and de Groot BL. Spontaneous quaternary and tertiary T-R transitions of human hemoglobin in molecular dynamics simulation. PLoS Comput.Biol. 6: e1000774 (2010) [pdf]
  15. Seeliger D and de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Computer-aided Molec.Design. 24: 417-422 (2010) [pdf]
  16. Seeliger D and de Groot BL. Protein thermostability calculations using alchemical free energy simulations. Biophys. J. 98: 2309-2316 (2010) [pdf]
  17. Groenhof G, Boggio-Pasqua M, and Robb MA. Computer Simulations of Photobiological Processes: the effect of the protein environment. Advanc. in Quantum Chem. 59: 181-212 (2010) [pdf]
  18. Fenton RA, Moeller HB, Nielsen S, de Groot BL, and Rützler M. A plate reader-based method for cell water permeability measurement. Am. J. Physiol - Renal Physiol. 298: F224-F230 (2010) [pdf]
  19. Seeliger D and de Groot BL. Conformational transitions upon ligand binding: Holo structure prediction from apo conformations. PLoS Comput. Biol. 6: e1000634 (2010) [pdf]
  20. De Boer TP, Nalos L, Stary A, Kok B, Houtman MJC, Antoons G, van Veen TAB, Beekman JDM, de Groot BL, Opthof T, Rook MB, Vos MA, and van der Heyden MAG. The antiprotozoic drug pentamidine blocks Kir2.x-mediated inward rectifier current by entering the cytoplasmic pore region. British J. of Pharmacol. 159: 1532-1541 (2010) [pdf]
  21. Stary A, Wacker S, Boukharta L, Zachariae U, Karimi-Nejad Y, Aqvist J, Vriend G, and de Groot BL. Toward a consensus model of the hERG potassium channel. ChemMedChem. 5: 455-467 (2010) [pdf]
  22. Doelker N, Zachariae U, and Grubmüller H. Hydrophilic Linkers and Polar Contacts Affect Aggregation of FG Repeat Peptides. Biophys. J. 98: 2653-2661 (2010) [pdf]
  23. Brakemann T, Weber G, Andresen M, Groenhof G, Stiel AC, Trowitzsch S, Eggeling C, Grubmüller H, Hell SW, Wahl MC, and Jakobs S. Molecular basis of the light-driven switching of the photochromic fluorescent protein Padron. JBC 285: 14603-14609 (2010) [pdf]
  24. Zink M and Grubmüller H. Primary changes of the mechanical properties of Southern Bean Mosaic Virus upon calcium removal. Biophys. J. 98: 687-695 (2010) [pdf]
  25. Hensen U, Lange O, Grubmüller H. Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach. PLoS ONE 5: e9179 (2010) [pdf]


2009
  1. Maksay G, Laube B, Schemm R, Grudzinska J, Drwal M, and Betz B. Different binding modes of tropeines mediating inhibition and potentiation of alpha 1 glycine receptors. J. of Neurochem. 109, 1725-1732 (2009) [pdf]
  2. Goette M, Grubmuller H. Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J. Comp. Chem.Vol 30, 447-456 (2009) [pdf]
  3. Hensen U, Grubmüller H, Lange O. Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. Phys. Rev. E. 80 (1): 011913 (2009) [pdf]
  4. Groenhof G, Schaefer LV, Boggio-Pasqua M, Robb MA. 
Excited state dynamics in biomolecules
In. Handbook of Mol. Biophys., Ed. H.Bohr Wiley, New York (2009)
  5. Kim S, Gailite I, Moussian B, Luschnig S, Goette M, Fricke K, Honemann-Capito M, Grubmüller H, Wodarz A. Kinase activity independent functions of atypical protein kinase C in Drosophila. J. of Cell Sci. 122: 3759-3771 (2009) [pdf]
  6. Boggio-Pasqua M, Robb MA, Groenhof G. Hydrogen bonding controls excited-state decay of the photoactive yellow protein chromophore. J. of the Am. Chem. Sci. 131: 13581-13581 (2009)
  7. De eiwitvouwbarrière De ingenieur 19: 36-39 (2009) [dutch-pdf]
  8. Haas J, Vöhringer-Martinez E, Bögehold A, Matthes D, Pelah A, Abel B, Grubmüller H. Primary steps pf pH-dependent insulin aggregation kinetics are governed by conformational flexibility. ChemBioChem 10: 1816-1822 (2009) [pdf] [Inside Cover]
  9. Hub JS, de Groot BL. Detection of functional modes in protein dynamics. PLoS Comp. Biol. 5: e1000480 (2009) [pdf]
  10. Zink M, Grubmüller H. Simulation of a Complete Viral Shell. InSiDE 7: 22-25 (2009) [pdf]
  11. Matthes D, de Groot BL. Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes. Biophys. J. 97: 599-608 (2009) [pdf] [supplement]
  12. Stegmann CM, Seeliger D, Sheldrick GM, de Groot BL, Wahl M. Thermodynamic signature of trapped water molecules in a protein-ligand interaction. Angew. Chem. 48: 5207-5210 (2009) [pdf]
  13. Fischer G, Kosinska-Eriksson U, Aponte-Santamaria C, Palmgren M, Geijer C, Hedfalk K, Hohmann S, de Groot BL, Neutze R, Lindkvist-Petersson K. Crystal Structure of a Yeast Aquaporin at 1.15A Reveals a Novel Gating Mechanism. PLoS Biol. 7: e1000130 (2009) [pdf]
  14. Goette M, Stumpe MC, Ficner R, Grubmüller H. Molecular Determinants of Snurportin 1 Ligand Affinity and Structural Response upon Binding. Biophys. J. 97: 581 - 589 (2009) [pdf]
  15. Donnini S, Villa A, Groenhof G, Mark AE, Wierenga RK, Juffer AH. Inclusion of ionization states of ligands in affinity calculations. Proteins: Structure, Function, and Bioinformatics 76: 138-150 (2009) [pdf]
  16. Stumpe M, Grubmüller H. Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophys. J. 96: 3744 - 3752 (2009) [pdf]
  17. Kubitzki MB, de Groot BL, Seeliger D. Protein dynamics: from structure to function. From Protein Structure to Function with Bioinformatics. pp. 217-249 (2009) [pdf]
  18. Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA. Predicting Free Energy Changes Using Structural Ensembles. Nature Methods. 6: 3-4 (2009) [pdf]
  19. Joshi HV, Jedrzejas MJ, de Groot BL. Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins 76: 30-46 (2009) [pdf]
  20. Portella G, de Groot, BL. Determinants of water permeability through nanoscopic hydrophilic channels. Biophys. J. 96: 925-938 (2009) [pdf] [new & notable pdf]
  21. Seeliger D, de Groot, BL. tCONCOORD-GUI: Visually Supported Conformational Sampling of Bioactive Molecules. J. Comp. Chem. 30: 1160-1166 (2009) [pdf]
  22. Reinhard F, Lange OF, Hub JS, Haas J, Grubmüller H. g_permute: Permutation-reduced phase space density compaction. Computer Physics Communications 180: 455-458 (2009) [pdf]
  23. Link O, Vöhringer-Martinez E, Lugovoj E, Liu Y, Siefermann K, Faubel M, Grubmüller H, Gerber RB, Miller Y, Abel B. Ultrafast phase transitions in metastable water near liquid interfaces. Faraday Discuss. 141: 67-79; discussion 81-98 (2009) [pdf]
  24. Zink M, Grubmüller H. Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys J. 96(4): 1350-63 (2009) [pdf]
  25. Hub JS, Grubmüller H, de Groot BL. Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? Handb Exp Pharmacol. 190: 57-76 (2009) [pdf]


2008
  1. Hayward S, de Groot BL. Normal modes and essential dynamics. Molecular modelling of proteins (2008)
  2. Fabiano E, Groenhof G, Thiel W. Approximate switching algorithms for trajectory surface hopping. Chem. Phys. 351: 111-116 (2008) [pdf]
  3. Lakomek NA, Lange OF, Walter KF, Farès C, Egger D, Lunkenheimer P, Meiler J, Grubmüller H, Becker S, de Groot BL, Griesinger, C. Residual dipolar couplings as a tool to study molecular recognition of ubiquitin. Biochem. Soc. Trans. 36(Pt 6): 1433-7 (2008) [pdf]
  4. Nagendran S, Sen SS, Roesky HW, Koley D, Grubmuller H, Pal A, Herbst-Irmer R. RGe(I)Ge(I)R Compound (R = PhC(NtBu)(2))with a Ge-Ge Single Bond and a Comparison with the Gauche Conformation of Hydrazine. Organometallics 27(21): 5459-63 (2008) [pdf]
  5. Stumpe MC, Grubmuller H. Polar or apolar - the role of polarity for urea-induced protein denaturation. PLoS. Comp. Biol. 4(11): e1000221 (2008) [pdf]
  6. Wozniak AK, Schroder GF, Grubmuller H, Seidel CA, Oesterhelt F. Single-molecule FRET measures bends and kinks in DNA. Proc. Natl. Acad. Sci. USA 105(47): 18337-42 (2008) [pdf]
  7. Lange OF, Grubmuller H. Full Correlation Analysis of Conformational Protein Dynamics. Proteins 70: 1294-1312 (2008) [pdf]
  8. Zachariae U, Grubmuller H. Importin-ß: Structural and Dynamic Determinants of a Molecular Spring. Structure 16: 906-915 (2008) [pdf]
  9. Kubitzki MB, de Groot BL. The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: a TEE-REX Molecular Dynamics Study. Structure 8: 1175-1182 (2008) [pdf]
  10. Portella G, Hub JS, Vesper MD, de Groot BL. Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels. Biophys. J. 95: 2275-2282 (2008) [pdf]
  11. Puchner EM, Alexandrovich A, Kho AL, Hensen U, Schafer LV, Brandmeier B, Grater F, Grubmuller H, Gaub HE, Gautel M. Mechanoenzymatics of titin kinase. PNAS 105: 13385-13390 (2008) [pdf]
  12. Bockmann RA, de Groot BL, Kakorin S, Neumann E, Grubmuller H. Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations. Biophysical J. 95: 1837-1850 (2008) [pdf]
  13. Lakomek NA, Walter KFA, Farès C, Lange OF, de Groot BL, Grubmuller H, Bruschweiler R, Munk A, Becker S, Meiler J, Griesinger C. Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics . J. Biomol. NMR 41: 139-155 (2008) [pdf] [support]
  14. Lange OF, Lakomek NA, Farès C, Schroder GF, Walter KFA, Becker S, Meiler J, Grubmuller H, Griesinger C, de Groot BL. Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution. Science 320: 1471-1475 (2008) [pdf] [support] [article1] [article2]
  15. Klyszejko AL, Shastri S, Mari SA, Grubmuller H, Muller DJ, Glaubitz C. Folding and Assembly of Proteorhodopsin JMB 376: 35-41 (2008) [pdf]
  16. Zachariae U, Schneider R, Velisetty P, Lange A, Seeliger D, Wacker SJ, Karimi-Nejad Y, Vriend G, Becker S, Pongs O, Baldus M, de Groot BL. The molecular mechanism of toxin-induced conformational changes in a potassium channel: relation to C-type inactivation. Structure. 16: 747-754 (2008) [pdf]
  17. Hartmann C, Chami M, Zachariae U, de Groot BL, Engel A, Grutter MG. Vacuolar protein sorting: Two different functional states of the AAA-ATPase Vps4p. J. Mol. Biol. 377: 352-363 (2008) [pdf]
  18. Muller EM, Hub JS, Grubmuller H, de Groot BL. Is TEA an inhibitor for human Aquaporin-1 ?. Pflugers Arch - Eur. J. Physiol. (2008) [pdf]
  19. Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4: 435-447 (2008) [pdf]
  20. Schafer LV, Groenhof G, Boggio-Pasqua M, Robb M, Grubmuller H. Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. PLoS Computational Biology 4: e1000034 (2008) [pdf]
  21. Groenhof G, Schafer LV, Boggio-Pasqua M, Grubmuller H, Robb MA. Arginine52 controls the photoisomerization process in Photoactive Yellow Protein J. Am. Chem. Soc. 130: 3250-3251 (2008) [pdf]
  22. Grubmuller H. Editorial: Wunderwerke der Evolution. Physik in unserer Zeit 1/08: 3 (2008) [pdf]
  23. Hub JS, de Groot BL. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc. Nat. Acad. Sci. 105: 1198-1203 (2008) [pdf]


2007
  1. Stumpe MC, Grubmüller H. Interaction of Urea with Amino Acids: Implications for Urea-Induced Protein Denaturation. J. Am.Chem.Soc. 129: 16126-16131 (2007) [pdf]
  2. Bouvier B, Grubmüller H. A Molecular Dynamics Study of Slow Base Flipping in DNA Using Conformational Flooding. Biophys. J. 93: 770-786 (2007) [pdf]
  3. Sieber JJ, Willig KI, Kutzner C, Gerding-Reimers C, Harke B, Donnert G, Rammner B, Eggeling C, Hell SW, Grubmüller H, Lang T. Anatomy and Dynamics of a Supramolecular Membrane Protein Cluster. Science 317: 1072-1076 (2007) [syntaxin-pdf] [header-pdf] [perspective-pdf] [supplement-pdf]
  4. Schäfer LV, Groenhof G, Klingen AR, Ullmann GM, Boggio-Pasqua M, Robb MA, Grubmüller H. Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra. Angew. Chemie Int. Ed. 119: 536-542 (2007) [pdf]
  5. Reinhard F, Grubmüller H. Estimation of absolute solvent and solvation shell entropies via permutation reduction. J. Chem. Phys. 126: 014102 (2007) [pdf]
  6. Schäfer LV, Müller EM, Gaub HE, Grubmüller H. Elastic properties of photoswitchable azobenzene polymers from molecular dynamics simulations. Angew. Chemie Int. Ed. 46: 2232-2237 (2007) [pdf] [supporting info]
  7. Gräter F, Grubmüller H. Fluctuations of primary ubiquitin folding intermediates in a force clamp. J. Struct. Biol. 157: 557-569 (2007) [pdf]
  8. Stumpe M, Grubmüller H. Aqueous urea solutions: Structure, energetics, and urea aggregation. J. Phys. Chem. B 111: 6220-6228 (2007) [pdf]
  9. Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt UW, de Groot BL, Grubmüller H. Speeding up parallel GROMACS on high-latency networks. J. Comp. Chem. 28: 2075-2084 (2007) [pdf]
  10. Groenhof G, Schäfer LV, Boggio-Pasqua M, Goette M, Grubmüller H, Robb MA. Ultrafast deactivation of an excited cytosine guanine base pair in DNA. J. Am. Chem. Soc. 129: 6812-6819 (2007) [pdf]
  11. Boggio-Pasqua M, Groenhof G, Schäfer LV, Grubmüller H, Robb MA. Ultrafast deactivation channel for thymine dimerization J. Am. Chem. Soc. 129: 10996-10997 (2007) [pdf]
  12. Grubmüller H, Schulten K. Editorial: Special issue: Advances in molecular dynamics simulations. J. Struct. Biol 157 (3): 443-443 (2007)
  13. Seeliger D, Haas J, de Groot BL. Geometry-based Sampling of Conformational Transitions in Proteins. Structure 15: 1482-1492 (2007) [pdf]
  14. Hub JS, Salditt T, Rheinstädter MC, de Groot BL. Short-range order and collective dynamics of DMPC bilayers. A comparison between molecular dynamics simulations, x-ray, and neutron scattering experiments. Biophys. J. 93: 3156-3168 (2007) [pdf]
  15. Vermeer LS, de Groot BL, Reat V, Milon A, Czaplicki J. Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments. Eur. Biophys. J. 36: 919-931 (2007) [pdf]
  16. Kubitzki MB, de Groot BL. Molecular Dynamics Simulations using Temperature Enhanced Essential dynamics Replica Exchange (TEE-REX). Biophys. J. 92: 4262-4270 (2007) [pdf]
  17. Portella G, Pohl P, de Groot BL. Invariance of Single-File Water Permeability in Gramicidin-like Peptidic Pores as function of Pore Length. Biophys. J. 92: 3930-3937 (2007) [pdf]
  18. Seeliger D, de Groot BL. Atomic contacts in protein structures. A detailed analysis of atomic radii, packing and overlaps. Proteins. 68: 595-601 (2007) [pdf]


2006
  1. Lange OF, Grubmüller H. Can Principal Components Yield a Dimension Reduced Description of Protein Dynamics on Long Time Scales ? J. Phys. Chem. B 110, 22842-22852 (2006) [pdf]
  2. Takamori S, Holt M, Stenius K, Lemke EA, Grønborg M, Riedel D, Urlaub H, Schenck S, Brügger B, Ringler Ph, Müller SA, Rammner B, Gräter F, Hub JS, de Groot BL, Mieskes G, Moriyama Y, Klingauf J, Grubmüller H, Heuser J, Wieland F, Jahn R. Molecular Anatomy of a Trafficking Organelle. Cell 127: 831-846 (2006) [pdf] [cover]
  3. Gräter F, de Groot BL, Jiang H, Grubmüller H. Ligand-Release Pathways in the Pheromone-Binding Protein of Bombyx mori. Structure 14: 1567-1576 (2006) [pdf]
  4. Gräter F, Xu W, Leal W, Grubmüller H. Pheromone Discrimination by the Pheromone-Binding Protein of Bombyx mori. Structure 14: 1577-1586 (2006) [pdf]
  5. Lange OF, Schäfer LV, Grubmüller H. Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics. J. Comput. Chem. 27: 1693-1702 (2006) [pdf]
  6. Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt UW, de Groot BL, Grubmüller H. Improved GROMACS scaling on ethernet switched clusters. Recent advances in parallel virtual machine and message passing interface, 13th European PVM/MPI User's Group Meeting, Bonn, Germany, September 17-20, 2006. Proceedings Series: Lecture Notes in Computer Science, B. Mohr, J. L. Träff, J. Worringen, J. Dongarra (Eds.) 404-405 [pdf]
  7. Zachariae U, Grubmüller H. A Highly Strained Nuclear Conformation of the Exportin Cse1p Revealed by Molecular Dynamics Simulations. Structure 14: 1469-1478 (2006) [pdf]
  8. Zachariae U, Grubmüller H. Prediction of a RanGTP-induced conformational switch in the exportin CAS/Cse1p by molecular dynamics simulations. MPIbpc News 5, 1-6 Max-Planck-Institut für biophysikalische Chemie (Göttingen) (2006) [pdf]
  9. Lange OF, Grubmüller H. Collective Langevin dynamics of conformational motions in proteins. J. Chem. Phys. 124: 214903 (2006) [pdf]
  10. Detmers FJM, de Groot BL, Müller EM, Hinton A, Konings IBM, Sze M, Flitsch SL, Grubmüller H, Deen PMT. Quaternary Ammonium Compounds as Water Channel Blockers. (2) J. Biol. Chem. 281: 14207-14214 (2006) [pdf]
  11. Sørensen JB, Wiederhold K, Müller EM, Milosevic I, Nagy G, de Groot BL, Grubmüller H, Fasshauer D. Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles. EMBO J. 25: 955-966 (2006) [pdf]
  12. de Groot BL, Böckmann RA, Grubmüller H. Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Physik in unserer Zeit 37: 73-79 (2006) [pdf] [cover]
  13. Lange OF, Grubmüller H. Generalized Correlation for Biomolecular Dynamics. Proteins: Structure, Function, and Bioinformatics 62: 1053-1061 (2006) [pdf]
  14. Grubmüller H, Seeger S, Tschesche H. Aufbau, Funktion und Diagnostik biogener Moleküle. In Bergmann/Schaefer, Lehrbuch der Experimentalphysik, Band 5: Gase, Nanosysteme, Flüssigkeiten, Karl Kleinermanns (Hrsg.), de Gruyter, Berlin pp. 977-1067 (2006)
  15. Stock G, Wachtveitl J, Grubmüller H. Editorial: Nonequilibrium dynamics in biomolecules. Chem Phys. 323 (1): 1-1 (Mar 31) (2006)
  16. Hub JS, de Groot BL. Does CO2 permeate through Aquaporin-1? Biophys. J. 91: 842-848 (2006) [pdf]
  17. Seeliger D, de Groot BL. Prediction of protein flexibility from geometrical constraints. Biotech International. 18: 20-22 (2006) [pdf]
  18. Rigden DJ, Littlejohn JE, Joshi HV, de Groot BL, Jedrzejas MJ. Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action. J. Mol. Biol. 358: 1165-1178 (2006) [pdf]
  19. Saparov SM, Pfeifer JR, Al-Momani L, Portella G, de Groot BL, Koert U, Pohl P. Mobility of a One-Dimensional Confined File of Water Molecules as a Function of File Length. Phys. Rev. Lett. 96: 148101 (2006) [pdf]


2005
  1. Van der Spoel D, Lindahl E, Hess B, Groenhof G, Merk AE, Berendsen HJC. GROMACS: Fast, Flexible, and Free. J. Comp. Chem. (2005) [pdf]
  2. Andresen M, Wahl MC, Stiel AC, Gräter F, Schäfer LV, Trowitzsch S, Weber G, Eggeling C, Grubmüller H, Hell SW, Jakobs S. Insight into the structure and mechanism of the reversible photoswitch of a fluorescent protein. MPIbpc news, Max-Planck-Institut für biophysikalische Chemie, Göttingen (2005) [pdf]
  3. Schröder GF, Alexiev U, Grubmüller H. Simulation of Fluorescence Anisotropy Experiments: Probing Protein Dynamics. Biophys. J. 89: 3757-3770 (2005) [pdf] [cover]
  4. Andresen M, Wahl MC, Stiel AC, Gräter F, Schäfer LV, Trowitzsch S, Weber G, Eggeling C, Grubmüller H, Hell SW, Jakobs S. Structure and mechanism of the reversible photoswitch of a fluorescent protein. PNAS 102: 13070-13074 (2005) [pdf]
  5. Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M. Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys. J. 89: 2113-2120 (2005) [pdf]
  6. Wozniak AK, Nottrott S, Kühn-Hölsken E, Schröder GF, Grubmüller H, Lührmann R, Seidel CAM, Oesterhelt F. Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements. RNA 11: 1545-1554 (2005) [pdf]
  7. Lange OF, Grubmüller H, de Groot BL. Molecular Dynamics Simulations of Protein G Challenge NMR-Derived Correlated Backbone Motions. Angew. Chem. Int. Ed. 44: 3394-3399 (2005) [pdf]
  8. de Groot BL, Grubmüller H. The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr. Opin. Struct. Biol. 15: 176-183 (2005) [pdf]
  9. Grubmüller H. Force probe molecular dynamics simulations. In U. Nienhaus, Editor Protein--Ligand Interactions p. 493-515, Totowa, NJ, USA, 2005. The Humana Press Inc
  10. Gräter F, Shen J, Jiang H, Gautel M, Grubmüller H. Mechanically Induced Titin Kinase Activation Studied by Force-Probe Molecular Dynamics Simulations. Biophys. J. 88: 790-804 (2005) [pdf]
  11. Nagy G, Milosevic I, Fasshauer D, Müller EM, de Groot BL, Lang T, Wilson MC, Sorensen JB. Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain. Molecular Biology of the Cell 16: 5675-5685 (2005) [pdf]
  12. Kukulski W, Schenk AD, Johanson U, Braun T, de Groot BL, Fotiadis D, Kjellbom P, Engel A. The 5 A structure of heterologously expressed plant Aquaporin SoPIP2;1. J. Mol. Biol. 350: 611-616 (2005) [pdf]
  13. Schenk AD, Werten PJL, Scheuring S, de Groot BL, Müller SA, Stahlberg H, Philippsen A, Engel A. The 4.5 A structure of human AQP2. J. Mol. Biol. 350: 278-289 (2005) [pdf]


2004
  1. de Meijere A, Schill H, Kozhushkov SI, Walsh R, Müller EM, Grubmüller H. Cyclopropylidenes, bicyclopropylidenes, and vinylcarbenes - some modes of formation and preparative applications. Russ. Chem. Bull., Intl. Ed. 53:947-959 (2004) [pdf] [russian]
  2. Jeney S, Stelzer EHK, Grubmüller H, Florin E-L. Mechanical Properties of Single Motor Molecules Studied by Three-Dimensional Thermal Force Probing in Optical Tweezers. Chem. Phys. Chem. 5: 1150-1158 (2004) [pdf]
  3. de Groot BL, Grubmüller H. Aquaporine: Die perfekten Wasserfilter der Zelle. BIOspektrum 4: 384-386 (2004) [pdf]
  4. Pöhlmann T, Böckmann RA, Grubmüller H, Uchanska-Ziegler B, Ziegler A, Alexiev U. Differential peptide dynamics is linked to Major Histocompatibility Complex polymorphism. J. Biol. Chem. 279: 28197-28201 (2004) [pdf]
  5. Grubmüller H. Proteins as molecular machines: Force probe simulations. In Norbert Attig, Kurt Binder, Helmut Grubmüller, and Kurt Kremer, Editors, Computational Soft Matter: From Synthetic Polymers to Proteins p. 401-421, Jülich, 2004. Forschungszentrum Jülich.
  6. Schröder GF, Grubmüller H. FRETsg: Biomolecular structure model building from multiple FRET experiments. Comput. Phys. Comm. 158: 150-157 (2004) [pdf]
  7. Böckmann RA, Grubmüller H. Multistep Binding of Divalent Cations to Phospholipid Bilayers: A Molecular Dynamics Study. Angew. Chemie Int. Ed. 43: 1021-1024 (2004) [pdf] [german] [cover]
  8. Rousseau R, Kleinschmidt V, Schmitt UW, Marx D. Unravelling protonation patterns in Bacteriorhodopsin by theoretical IR spectroscopy. Angewandte Chemie Int. 43: 4804-4807 (2004)
  9. Rousseau R, Kleinschmidt V, Schmitt UW, Marx D. Modeling protonated water networks in Bacteriorhodopsin. Phys. Chem. Chem. Phys. 6: 1848 (2004)


2003
  1. Margittai M, Widengren J, Schweinberger E, Schröder GF, Fasshauer D, Felekyan S, Haustein E, König M, Grubmüller H, Jahn R, Seidel CAM. Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. PNAS 100: 15516-15521 (2003) [pdf] [supplement]
  2. Schröder GF, Grubmüller H. Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments. J. Chem. Phys. 119: 9920-9924 (2003) [pdf]
  3. de Groot BL, Frigato T, Helms V, Grubmüller H. The mechanism of proton exclusion in the aquaporin-1 water channel. J. Mol. Biol. 333: 279-293 (2003) [pdf]
  4. Böckmann RA, Grubmüller H. Conformational dynamics of the F1-ATPase ß-subunit: A molecular dynamics study. Biophys. J. 85: 1482-1491 (2003) [pdf] [cover]
  5. Böckmann RA, Hac A, Heimburg T, Grubmüller H. Effect of sodium chloride on a lipid bilayer. Biophys. J. 85: 1647-1655 (2003) [pdf]
  6. Grubmüller H. What happens if the room at the bottom runs out? A close look at small water pores. Proc. Natl. Acad. Sci. (Commentary) 100: 7421-7422 (2003) [pdf]
  7. Knecht V, Grubmüller H. Mechanical Coupling via the Membrane Fusion SNARE Protein Syntaxin-1A: A Molecular Dynamics Study. Biophys. J. 84: 1527-1547 (2003) [pdf]
  8. de Groot BL, Engel A, Grubmüller H. The structure of the Aquaporin-1 water channel: a comparison between cryo-electron microscopy and x-ray crystallography. J. Mol. Biol. 325: 485-493 (2003) [pdf]


2002
  1. Werten PJL, Remigy H-W, de Groot BL, Fotiadis D, Philippsen A, Stahlberg H, Grubmüller H, Engel A. Progress in the analysis of membrane protein structure and function. FEBS Lett. 529: 65-72 (2002) [pdf]
  2. Fujiyoshi Y, Mitsuoka K, de Groot BL, Philippsen A, Grubmüller H, Agre P, Engel A. Structure and function of water channels. Curr. Opin. Struct. Biol. 12: 509-515 (2002) [pdf]
  3. Jahn R, Grubmüller H. Membrane fusion. Curr. Opin. Cell Biol. 14: 488-495 (2002) [pdf]
  4. de Groot BL, Tieleman DP, Pohl P, Grubmüller H. Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study. Biophys. J. 82: 2934-2942 (2002) [pdf] [cover]
  5. Rief M, Grubmüller H. Force spectroscopy of single biomolecules. Chem. Phys. Chem. 3: 255-261 (2002) [pdf] [cover]
  6. Böckmann R, Grubmüller H. Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase. Nature Struct. Biol. 9: 198-202 (2002) [pdf]
  7. Müller EM, de Meijere A, Grubmüller H. Predicting unimolecular chemical reactions: Chemical flooding. J. Chem. Phys. 116: 897-905 (2002) [pdf]
  8. Mello LV, de Groot BL, Li S, Jedrzejas MJ. Structure and flexibility of streptococcus agalactiae hyaluronate lyase complex with its substrate: Insights into the mechanism of processive degradation of hyaluronan. J. Biol. Chem. 277: 36678-36688 (2002) [pdf]
  9. Jedrzejas MJ, Mello LV, de Groot BL, Li S. Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase: Structures of complexes with the substrate. J. Biol. Chem. 277: 28287-28297 (2002) [pdf]
  10. Schmitt UW, Voth GA. A second generation multistate empirical valence bond model for proton transport in aqueous systems. J. Chem. Phys. 117: 5839 (2002)
  11. Kim J, Schmitt UW, Gruetzmacher JA, Scherer NE, Voth GA. The vibrational spectrum of the hydrated proton: Comparison of experiment, simulation, and normal mode analysis. J. Chem. Phys. 116: 738 (2002)


2001
  1. de Groot BL, Grubmüller H. Water permeation across biological membranes: Mechanism and dynamics of Aquaporin-1 and GlpF. Science 294: 2353-2357 (2001) [pdf]
  2. de Groot BL, Engel A, Grubmüller H. A refined structure of human Aquaporin 1. FEBS Lett. 504: 206-211 (2001) [pdf]
  3. Heymann B, Grubmüller H. Molecular dynamics force probe simulations of antibody/antigen unbinding: Entropic control and non-additivity of unbinding forces. Biophys. J. 81: 1295-1313 (2001) [pdf]
  4. de Groot BL, Daura X, Mark AE, Grubmüller H. Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. J. Molec. Biol. 309: 299-313 (2001) [pdf]
  5. Rief M, Grubmüller H. Kraftspektroskopie von einzelnen Biomolekülen. Physikalische Blätter pages 55-61, Feb. (2001) [pdf]
  6. Brewer ML, Schmitt UW, Voth GA. The formation and dynamics of proton wires in channel environments. Biophysical J. 80: 1691 (2001)
  7. Cuma M, Schmitt UW, Voth GA. A multi-state empirical valence bond model for weak acid dissociation in aqueous systems. J. Phys. Chem. A 105: 2814 (2001)


2000
  1. Böckmann R, Grubmüller H. Energy transfer in F1-ATPase studied by molecular dynamics simulations. Europ. Biophys. J. 29: 337 (2000)
  2. Böckmann R, Grubmüller H. Elastic properties of secondary structure elements: A molecular dynamics study. Europ. Biophys. J. 29: 381 (2000)
  3. Stahlberg H, Braun T, de Groot B, Philippsen A, Borgnia MJ, Agre P, Kühlbrandt W, Engel A. The 6.9A structure of GlpF: a basis for homology modeling of the glycerol channel from E. Coli. J. Struct. Biol. 132: 133-141 (2000) [pdf]
  4. Heymann JB, Pfeiffer M, Hildebrand V , Kaback HR, Fotiadis D, de Groot BL, Engel A, Oesterhelt D, Müller DJ. Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Struct. Fold. Des. 8: 643-653 (2000) [pdf]
  5. Ossig R, Schmitt HD, de Groot BL, Riedel D, Keränen S, Ronne H, Grubmüller H, Jahn R. Exocytosis requires asymmetry in the central layer of the snare complex. EMBO J. 19: 6000-6010 (2000) [pdf]
  6. Schulze BG, Grubmüller H, Evanseck JD. Functional significance of hierarchical tiers in carbonmonoxy myoglobin: Conformational substates and transitions studied by conformational flooding simulations. J. Am. Chem. Soc. 122: 8700-8711 (2000) [pdf]
  7. de Groot BL, Heymann JB, Engel A, Mitsuoka K, Fujiyoshi Y, Grubmüller H. The fold of human Aquaporin 1. J. Molec. Biol. 300: 987-994 (2000) [pdf]
  8. Heymann B, Grubmüller H. Dynamic force spectroscopy of molecular adhesion bonds. Phys. Rev. Lett. 84: 6126-6129 (2000) [pdf] [postscript]
  9. Stahlberg H, Braun T, de Groot B, Philippsen A, Borgnia MJ, Agre P, Kuhlbrandt W, Engel A. The 6.9-angstrom structure of GlpF: A basis for homology modeling of the glycerol channel from Escherichia coli. J. Struct. Biol. 132 (2): 133-141 (2000) [pdf]
  10. Heymann JB, Pfeiffer M, Hildebrandt V, Kaback HR, Fotiadis D, de Groot BL, Engel A, Oesterhelt D, Müller DJ. Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Struct. Fold. Des. 8(6): 643-653 (2000) [pdf]
  11. Schmitt UW, Voth GA. The Isotope Substitution Effect on the Hydrated Proton. Chem. Phys. Lett. 329: 36 (2000)
  12. Day TJ, Schmitt UW, Voth GA. The mechanism of hydrated proton transport in water. J. Am. Chem. Soc. 122: 12027 (2000)
  13. Cuma M, Schmitt UW, Voth GA. A multi-state empirical valence bond model for acid-base chemistry in aqueous systems. Chem. Phys. 258: 187-199 (2000)


1999
  1. Eichinger M, Heller H, Grubmüller H. EGO - An efficient molecular dynamics program and its application to protein dynamics simulations. In Rüdiger Esser, Peter Grassberger, Johannes Grotendorst, and Marius Lewerenz, editors, Workshop on Molecular Dynamics on Parallel Computers, John von Neumann Institute for Computing (NIC) Research Centre Jülich, Germany, 8-10 February 1999 397-402, World Scientific, Singapore 912805
  2. Heymann B, Grubmüller H. Elastic properties of poly(ethylene-glycol) studied by molecular dynamics stretching simulations. Chem. Phys. Lett. 307: 425-432 (1999) [pdf]
  3. Moffat K, Changeux J-P, Crothers DM, Grubmüller H, Nienhaus GU, Palma MU, Parak FG, Schulten K, Warshel A. How does complexity lead to apparently simple function? In H. Frauenfelder, J. Deisenhofer, and P. Wolynes, editors (1999) Simplicity and Complexity in Proteins and Nucleic Acids, Dahlem Workshop Reports 255-280, Dahlem University Press, Berlin
  4. Grubmüller H, Heymann B. Proteindynamik von Ligand/Rezeptor-Bindungen. MPIbpc news, Max-Planck-Institut für biophysikalische Chemie, Göttingen (1999) [pdf]
  5. Heymann B, Grubmüller H. 'Chair-boat' transitions and side groups affect the stiffness of polysaccharides. Chem. Phys. Lett. 305: 202-208 (1999) [pdf]
  6. Heymann B, Grubmüller H. AN02/DNP unbinding forces studied by molecular dynamics AFM simulations. Chem. Phys. Lett. 303: 1-9 (1999) [pdf]
  7. Amadei A, de Groot BL, Ceruso M-A, Di Nola A, Berendsen HJC. A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells. PROTEINS: Struct. Funct. Gen. 35: 283-292 (1999) [pdf] [abstract]
  8. de Groot B. Native state protein dynamics. PhD Thesis, University of Groningen (1999) [pdf]
  9. de Groot BL, Vriend G, Berendsen HJC. Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism. J. Mol. Biol. 286: 1241-1249 (1999) [pdf] [abstract]
  10. Schmitt UW, Voth GA. Quantum properties of the excess proton in liquid water Isr. J. Chem. 39: 483 (1999)
  11. Schmitt UW, Voth GA. The computer simulation of proton transport in water. J. Chem. Phys. 111: 9 (1999)


1998
  1. Grubmüller H, Tavan P. Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they? J. Comp. Chem. 19: 1534-1552 (1998) [pdf]
  2. Eichinger M, Heymann B, Heller H, Grubmüller H, Tavan P. Conformational dynamics simulations of proteins. In P. Deuflhard, J. Hermans, B. Leimkuhler, A. E. Mark, S. Reich, and R. D. Skeel, editors Lecture Notes in Computational Science and Engineering (Vol 4). Computational Molecular Dynamics: Challenges, Methods, Ideas 78-97, Springer (1998) [pdf]
  3. Langedijk JPM, de Groot BL, Berendsen HJC, van Oirschot JT. Structural homology of the central conserved region of the attachment protein G of the respiratory syncytial virus with the fourth subdomain of 55 kD tumor necrosis factor receptor. Virology 243: 293-302 (1998) [pdf]
  4. de Groot BL, Hayward S, van Aalten DMF, Amadei A, Berendsen HJC. Domain motions in bacteriophage T4 Lysozyme; a comparison between Molecular Dynamics and Crystallographic Data PROTEINS: Struct. Funct. Gen. 31: 116-127 (1998) [pdf] [html]
  5. Brickmann J, Schmitt UW. Classical molecular dynamics simulations with quantum degrees of freedom. Proceedings of the NATO ASI "Advances in the Computer Simulations of Liquid Crystals (1998)", Erice
  6. Schmitt UW, Voth GA. A multi-state empirical valence bond model for proton transport in water. J. Phys. Chem. B. 102: 5547 (1998)


1997
  1. Grubmüller H, Heymann B, Tavan P. Simulation eines molekularen Erkennungsvorgangs. Spektrum der Wissenschaft 14-16, März (1997)
  2. Eichinger M, Grubmüller H, Heller H, Tavan P. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations. J. Comp. Chem. 18:1729-1749 (1997) [pdf] [postscript] [html]
  3. Grubmüller H, Heymann B. Microscopic interpretation of AFM single molecule rupture experiments by molecular dynamics simulations. In Christian Colliex, Andreas Engel, and Jean Fourmentin-Guilbert, editors Proceedings of the Workshop `STM - AFM - SNOM: New Nanotools for Molecular Biology', April 16th-18th, 1997 pages III 45-50, Fondation Fourmentin-Guilbert, 93160 Noisy Le Grand (France)
  4. de Groot BL, van Aalten DMF, Scheek RM, Amadei A, Vriend G, and Berendsen HJC. Prediction of protein conformational freedom from distance constraints. PROTEINS: Struct. Funct. Gen. 29: 240-251 (1997) [pdf] [abstract]
  5. van Aalten DMF, Conn DA, de Groot BL, Findlay JBC, Berendsen HJC, Amadei A. Protein dynamics derived from clusters of crystal structures. Biophys. J. 73(6): 2891-2896 (1997)
  6. van Aalten DMF, de Groot BL, Berendsen HJC, Findlay JBC, Amadei A. A Comparison of techniques for calculating Protein Essential Dynamics. J. Comp. Chem. 18:169-181 (1997) [pdf]
  7. Hankel M, Karasözen B, Rentrop P, Schmitt U. A molecular dynamics model for symplectic integrators. Mathematical Modelling of Systems 3: 282-296 (1997)


1996
  1. Grubmüller H, Heymann B, Tavan P. Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force. Science 271: 997-999 (1996) [pdf] [postscript] [html]
  2. van Aalten DMF, de Groot BL, Berendsen HJC, Findlay JBC. Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins. The biochemical journal 319(2): 543-550 (1996) [pdf]
  3. van der Spoel D, de Groot BL, Hayward S, Berendsen HJC, Vogel HJ. Bending of the Calmodulin Central Helix: A theoretical study. Prot. Sci. 5: 2044-2053 (1996) [abstract]
  4. de Groot BL, Amadei A, Scheek RM, van Nuland NAJ, Berendsen HJC. An extended sampling of the configurational space of HPr from E. coli. PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) [abstract]
  5. de Groot BL, van Aalten DMF, Amadei A, Berendsen HJC. The consistency of large concerted motions in proteins in Molecular Dynamics simulations. Biophys. J. 71: 1707-1713 (1996) [pdf] [abstract]
  6. van Nuland NAJ, Wiersma JA, van der Spoel D, de Groot BL, Scheek RM, Robillard GT. Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement. Prot. Sci. 5: 442-446 (1996)
  7. de Groot BL, Amadei A, van Aalten DMF, Berendsen HJC. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J. Biomol. Struct. Dyn. 13 : 741-751 (1996) [abstract]
  8. Amadei A, Linssen ABM, de Groot BL, van Aalten DMF, Berendsen HJC. An efficient method for sampling the essential subspace of proteins. J. Biomol. Struct. Dyn. 13:615-626 (1996) [abstract]
  9. Schmitt U, Brickmann J. The photodissociation/recombination dynamics of I2 in an Ar matrix: Wave packet propagation in a mixed quantum-classical picture . J. Mol. Mod. 2: 300-303 (1996)
  10. Schmitt U, Brickmann J. Discrete time-reversible propagation scheme for mixed quantum-classical dynamics. Chem. Phys. 45: 208 (1996)


1995
  1. Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. (2) (3) (4) Phys. Rev. E 52: 2893-2906 (1995) [pdf] [postscript] [html]
  2. Eichinger M, Grubmüller H, Heller H, Tavan P. Fast molecular dynamics simulation on a Parsytec PowerXplorer system. User report, Heinrich-Heine-Universität, Universitätsrechenzentrum / Parsytec Computer GmbH, Universitätsstr., 40225 Düsseldorf, Germany, June (1995)
  3. Eichinger M, Grubmüller H, Heller H. User Manual for EGO_VIII, Release 2.0. (2) (3) (1995) [html]
  4. Scheek RM, van Nuland NAJ, de Groot BL, Amadei A. Structure from NMR and molecular dynamics: distance restraining inhibits motion in the essential subspace. J. Biomol. NMR. 6:106-11 (1995)
  5. Amadei A, Linssen ABM, de Groot BL, Berendsen HJC. Essential degrees of freedom of proteins. in Modelling of Biomolecular Structures and Mechanismsm A. Pullmann et. al. (ed.) 85-93 (1995)


1994
  1. Grubmüller H, Ehrenhofer N, Tavan P. Conformational dynamics of proteins: Beyond the nanosecond time scale. In M. Peyard, editor, Proceedings of the Workshop `Nonlinear Excitations in Biomolecules', May 30-June 4, 1994, Les Houches (France) 231-240. Centre de Physique des Houches (France), Springer-Verlag [postscript] [html]
  2. Grubmüller H. Proteine: Einblicke in ihre Funktionsweise. 'Spektrum Videothek', Sept. 1994. Spektrum akademischer Verlag, Heidelberg (Germany)
  3. Grubmüller H. Molekulardynamik von Proteinen auf langen Zeitskalen. PhD thesis, Technische Universität München, Jan (1994) [pdf] [postscript]
  4. Grubmüller H, Tavan P. Molecular dynamics of conformational substates for a simplified protein model. J. Chem. Phys. 101: 5047-5057 (1994) [pdf] [postscript] [html]


1993
  1. Grubmüller H, Döhring K, Tavan P, Nonella M, Oesterhelt D. BR AT WORK: A computeranimation for the 13-14-cis-model of the photochemical cycle of bacteriorhodopsin. Journal of Molecular Graphics 11(4):258 (1993)
  2. Böhm MC, Schmitt U, Schütt J. Correlation effects and charge fluctuations in pi-systems. A combined PPP and localized many-particle analysis. J. Phys. Chem. 97: 11427-11434 (1993)


1992
  1. Grubmüller H. On the suitability of efficient many-body algorithms for molecular dynamics simulations of biological macromolecules. In K. I. M. McKinnon and F. Plab, editors, Proceedings of the Second Parallel Numerical Analysis Workshop, June 25-26, Edinburgh, UK 226-238. Edinburgh Parallel Computing Centre, University of Edinburgh (1992)


1991
  1. Tavan P, Grubmüller H. Selbstorganisation von Assoziativspeichern und Musterklassifikatoren: Rekurrente Signalverarbeitung auf topologischen Merkmalskarten. In Kleinheubacher Berichte, Bd. 34 573-582, Forschungsinstitut beim FTZ, Darmstadt. DBP Telekom (1991)
  2. Grubmüller H, Heller H, Windemuth A, Schulten K. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Molecular Simulation 6: 121-142 (1991) [pdf]


1990
  1. Tavan P, Grubmüller H, Kühnel H. Self-organization of associative memory and pattern classification: Recurrent signal processing on topological feature maps. Biological Cybernetics 64(2): 95-105 (1990)
  2. Boehncke K, Heller H, Grubmüller H, Schulten K. Molecular dynamics simulations on a systolic ring of transputers. In Alan S. Wagner, editor, Transputer Research and Applications 3 83-94. North American Transputer Users Group, IOS Press, Van Diemenstraat 94, 1013 CN Amsterdam, The Netherlands (1990)
  3. Heller H, Grubmüller H, Schulten K. Molecular dynamics simulation on a parallel computer. Molecular Simulation 5: 133-165 (1990) [pdf]


1989
  1. Grubmüller H. Dynamiksimulation sehr großer Makromoleküle auf einem Parallelrechner. Master's thesis, Technische Universität München (1989)


1988
  1. Grubmüller H, Heller H, Schulten K. Eine CRAY für 'jedermann'. mc (11): 48-65, November (1988) [pdf] [cover]


PhD / Diploma theses at the department
  1. Dirk Matthes Spontaneous aggregation of fibril-forming peptides studied by Molecular Dynamics simulations PhD thesis, Chemics, 2011
  2. Martin Hoefling Simulations and Experiments: How close can we get? PhD thesis, Physics, 2011 [pdf]
  3. Andreas Russek Simulation von Nucleoporin-Netzwerken Diploma thesis, Physics, 2011 [pdf]
  4. Christian Kappel Structure and Dynamics of Proteins under Force PhD thesis, Physics, 2011 [pdf]
  5. Stephanus Fengler Estimating Orientational Water Entropy At Protein Interfaces. PhD thesis, Physics, 2011
  6. Camilo Aponte Understanding the molecular machinery of aquaporins through molecular dynamics simulations. PhD thesis, Physics, 2011 [pdf]
  7. Béla Voß The Ligand Binding Mechanism of the MloK1 Ion Channel. Diploma thesis, Physics, 2010 [pdf]
  8. Michal Walczak Bayesian orientation estimate from single molecule x-ray scattering data. Diploma thesis, Physics, 2010 [pdf]
  9. David Köpfer Struktur-Aktivitätsbeziehungen in Membranproteinen: Berechnung von Blockeraktivitäten in hERG-Ionenkanälen. Diploma thesis, Physics, 2010
  10. Frank Wiederschein Investigation of Laser-Induced-Liquid-Beam-Ion-Desorption (LILBID) with Molecular Dynamics Simulations. PhD thesis, Physics, 2010 [pdf]
  11. Carl Friedrich Burmeister Interaction of Short X-ray Pulses with Biomolecules. Diploma thesis, Physics, 2009 [pdf]
  12. Christian Blau Effect of posttranscriptional modifications and Mg2+ ions on tRNA structure and flexibility. Diploma thesis, Physics, 2009 [pdf]
  13. Mareike Zink Mechanical Properties of Icosahedral Viral Shells. A Molecular Dynamics Study. PhD thesis, Physics, 2009 [pdf]
  14. Ulf Hensen Thermodynamic Driving Forces in Protein Regulation Studied by Molecular Dynamics Simulations. PhD thesis, Chemistry, 2009 [pdf]
  15. Sören Wacker Molecular Dynamics Study of Potassium Channels, their Interaction with Non-Amino Acid Compounds and Peptidic Scorpion Toxins. Diploma thesis, Physics, 2008 [pdf]
  16. Martin Vesper Verfeinerung der Proteinkristallographie durch Flexibilitätsvorhersagen. Diploma thesis, Physics, 2008
  17. Maik Götte Free energy calculations of protein-ligand complexes with computational molecular dynamics. PhD thesis, Biology, 2008 [pdf]
  18. Esteban Vöhringer-Martinez Dynamics, ionization and charge separation in superheated metastable water. PhD thesis, Chemistry, 2008 [pdf]
  19. Florian Tegeler Dynamic Protonation of Titrable Groups in Biomolecules for Molecular Dynamics Simulations. Diploma thesis, Physics, 2008 [pdf]
  20. Guillem Portella Determinants of water and ion permeation through nanopores studied by Molecular Dynamics simulations. PhD thesis, Chemistry, 2008 [link]
  21. Daniel Seeliger Geometry-based Conformational Sampling of Proteins. PhD thesis, Chemistry, 2008 [pdf]
  22. Jochen Hub Selectivity, Regulation, and Inhibition of Aquaporin Channels. A Molecular Dynamics Study. PhD thesis, Physics, 2008 [pdf]
  23. Marcus Kubitzki Enhanced Conformational Sampling of Proteins Using TEE-REX. PhD thesis, Physics, 2007 [link]
  24. Lars Bock Molecular Dynamics Simulations of the Nascent Peptide Chain in the Ribosomal Exit Tunnel. Diploma thesis, Physics, 2007
  25. Martin Stumpe De natura denaturantium - On the molecular basis of urea-induced protein denaturation. PhD thesis, Physics, 2007 [pdf]
  26. Marcus Hennig Preserving Transformation Method for the Computation of Solvent Entropies. Diploma thesis, Physics , 2007 [pdf]
  27. Lars Schäfer Photoactivated Processes in condensed Phase studied by Molecular Dynamics Simulations. PhD thesis, Chemistry, 2007 [pdf]
  28. Florian Dommert The Unfolding Pathway of Ubiquitin in various chemical environments. Diploma thesis, Physics, 2007 [pdf]
  29. Christian Kappel Enforced Unfolding of Bacteriorhodopsin via Force Probe Molecular Dynamics. Diploma thesis, Physics, 2007 [pdf]
  30. Harshad Joshi Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase: A Molecular Dynamics Study. PhD thesis, Physics, 2007 [pdf]
  31. Martin Meling Modellierung und Strukturanalyse von b-Faltblattkristalliten in Spinnenseide Diploma thesis, Physics, 2006 [pdf]
  32. Oliver Lange Collective Langevin Dynamics of Conformational Motions in Protein PhD thesis, Physics, 2005 published with  Cuvillier Verlag [pdf]
  33. Frauke Gräter Enforced functional protein motions studied by Molecular Dynamic. PhD thesis, Chemistry , 2005 [pdf]
  34. Friedemann Reinhard Computation of solvent entropies from molecular dynamics simulations. Diploma thesis, Physics, 2005 [pdf]
  35. Gunnar Schröder Simulation of Fluorescence Spectroscopy Experiments. PhD thesis, Physics, 2004 [pdf]
  36. Volker Knecht Membrane Fusion SNARE Protein Syntaxin-1A: A Molecular Dynamics Study. PhD thesis, Physics; Mensch und Buch Verlag, Berlin 2003 [pdf]
  37. Helmut Grubmüller Theorie und Simulation induzierter Konformationsdynamik von Proteinen postdoctoral lecture qualification (Habilitation) Physics, 2002 [pdf]
  38. Jr-hung Lin Untersuchung der dielektrischen Relaxation von Wasser durch Molekulardynamiksimulation. Diploma thesis, Physics, 2002 [pdf]
  39. Rainer Böckmann Molekulare Dynamik von Proteinen: Von der a-Helix zur ATP Synthase. PhD thesis Physics, 2002 [pdf]
  40. Matthias Müller Molekular-Dynamik-Simulationen zum Katalyse-Mechanismus der Acetylcholinesterase. PhD thesis, Physics, 2002 [pdf]
  41. Gunnar Schröder Molekulardynamiksimulation der Flexibilität und Fluoreszenzanisotropie eines an ein Protein gebundenen Farbstoffs. Diploma thesis, Physics, 2001 [pdf]
  42. Berthold Heymann Molekulardynamiksimulationen kraftmikroskopischer Einzelmolekülexperimente. PhD thesis, Physics, 2000 [pdf]


Bachelor/Master theses at the department
  1. Fabian Knoch Steering excited state dynamics of biological chromophores by external electric fields. Bachelor thesis, Physics, 2011 [pdf]
  2. Timo Graen Anharmonic Infrared Spectra from Short - QM/MM Simulations. Master thesis, Physics, 2011 [pdf]
  3. Timo Graen Dye'ing for FRET: The HTH motif in smFRET-MD Simulation. Bachelor thesis, Physics, 2009 [pdf]
  4. René Rex Quantification of structure/dynamics correlation of globular proteins. Master thesis, Appl. Inform., 2009 [pdf]



Jan 11, 2012

The information on this page is part of the CV of Helmut Grubmüller, Bert de Groot, and Gerrit Groenhof.

© 2011, Max Planck Institute for Biophysical Chemistry, Göttingen