Department of Theoretical and Computational Biophysics

Publications of the Department


    1. Aponte-Santamaria C, Fischer G, Bath P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci. Reports 7, 4016 (2017) [pdf] [supplement]
    2. Ban D, Smith CA. de Groot BL, Griesinger C, Lee D. Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Archives of Biochem. and Biophys. 628, 81-91 (2017) [pdf]
    3. Briones R, Aponte-Santamaria C, de Groot BL. Localization and ordering of lipids around Aquaporin-0: Proteinand lipid mobility effects. Frontiers in Physiology 8 (124), 1-9 (2017) [pdf]
    4. Czub J, Wieczór M, Prokopowicz B, Grubmüller H. Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F1‑ATPase. J. Am. Chem. Soc. 139, 4025−4034 (2017) [pdf] [supplement]
    5. Dobrev P, Donnini S, Groenhof G, Grubmüller H. Accurate three states model for amino acids with two chemically coupled titrating sites in explicit solvent atomistic constant pH simulations and pKa calculations. J. Chem. Theory Comput. 13 (1), 147-160 (2017) [pdf] [supplement]
    6. Gajewski J, Buelens F, Serdjukow S, Janßen M, Cortina N, Grubmüller H, Grininger M. Engineering fatty acid synthases for directed polyketide production. Nature Chem. Biol. 13, 363–365 (2017) [pdf] [supplement]
    7. Gapsys V, de Groot BL. pmx Webserver: A user friendly interface for Alchemistry. J. Chem. Inf. Model. 57 (2), pp 109–114 (2017) [pdf] [supplement]
    8. Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD (jr). Charmm 36m: an improved force field for folded and intrinsically disordered proteins. Nature Meth. 14, 71-73 (2017) [pdf] [supplement]
    9. Machtens JP, Briones R, Alleva C, de Groot BL, Fahlke C. Gating charge calculations by computational electrophysiology simulations. Biophys. J. 112 (7), pp. 1396-1405 (2017) [pdf]
    10. Saboe PO, Rapisarda C, Kaptan S, Hsiao YS, Summers R, De Zorzi R, Dukovski D, Yu J, de Groot BL, Kumar M, Walz T. Role of pore-lining residues in defining the rate of water conduction by Aquaporin-0. Biophys. J. 112 (5), pp. 953-965 (2017) [pdf+supplement] [supplement]
    11. NEW: Ukmar-Godec T, Bertinetti L, Dunlop J, Godec A, Grabiger M, Masic A, Nguyen H, Zlotnikov I, Zaslansky P, Faivre D. A tooth without mineral: materials nano architecturing via cation-mediated protein assembly. Adv. Mater. 1701171 (2017) [pdf]
    12. Yin Z, Inhester L, Thekku Veedu S, Quevedo W, Pietzsch A, Wernet P, Groenhof G, Föhlisch A, Grubmüller H, Techert S. Cationic and anionic impact on the electronic structure of liquid water. J. Phys. Chem. Let. 8, pp. 3759-3764 (2017) [pdf] [supplement]


    1. Arenz S, Bock LV, Graf M, Innis CA, Beckmann R, Grubmüller H, Vaiana AC, Wilson DN. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nature Comm. 7, 12026 (2016) [pdf] [supplement] [Reviewers' Comments]
    2. Assentoft M, Kaptan S, Schneider HP, Deitmer JW, de Groot BL, MacAulay N. Aquaporin 4 as a NH3 Channel. J. Biol. Chem. 291 (36), 19184–19195 (2016) [pdf]
    3. Briones R, Weichbrodt C, Paltrinieri L, Mey I, Villinger S, Giller K, Lange A, Zweckstetter M, Griesinger C, Becker S, Steinem C, de Groot BL. Voltage Dependence of Conformational and Subconducting States of VDAC-1 Dynamics. Biophys J. 111, 1223–1234 (2016) [pdf] [supplement] [pdf+supplement]
    4. Bubnis G, Risselada HJ, Grubmüller HG. Exploiting Lipid Permutation Symmetry to Compute Membrane Remodeling Free Energies. Phys. Rev. Lett. 117, 188102 (2016) [pdf] [supplement]
    5. Donnini S, Ullmann RT, Groenhof G, Grubmüller H. Charge-neutral constant pH molecular dynamics simulations using a parsimonious proton buffer. J. Chem. Theory Comput. 12 (3), 1040-1051 (2016) [pdf]
    6. Fischer N, Neumann P, Bock LV, Maracci C, Wang Z, Paleskava A, Konevega AL, Schröder GF, Grubmüller H, Ficner R, Rodnina MV, Stark H. The pathway to GTPase activation of elongation factor SelB on the ribosome. Nature 540 (7631), 80-85 (2016) [pdf]
    7. Gapsys V, Michielssens S, Seeliger D, de Groot BL. Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angew. Chem. 55 (26), pp. 7364-7368 (2016) [pdf] [supplement]
    8. Graen T, Grubmüller H. NuSol: Numerical solver for the 3D stationary nuclear Schrödinger equation. Comput. Phys. Comm. 198, 169-178 (2016) [pdf]
    9. Graen T, Inhester L, Clemens M, Grubmüller H, Groenhof G. The Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution. J. Am. Chem. Soc. 138, 16620−16631 (2016) [pdf]
    10. Ilgü H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, and Fotiadis D. Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proc. Nat. Acad. Sci. 113 (37), 10358–10363 (2016) [pdf]
    11. Kirscht A, Kaptan S, Bienert GP, Chaumont F, Nissen P, de Groot BL, Kjellbom P, Gourdon P, Johanson U. Crystal structure of an ammonia-permeable aquaporin. PLOS Biol. 14 (3), 1-19 (2016) [pdf]
    12. Kumar R, Grubmüller H. Phi29 Connector-DNA Interactions Govern DNA Crunching and Rotation, Supporting the Check-Valve Model. Biophys. J. 110, 455–469 (2016) [pdf] [supplement] [pdf+supplement]
    13. Kutzner C, Köpfer D, Machtens JP, de Groot BL, Song C, Zachariae U. Insights into the function of ion channels by computational electrophysiology simulations. BBA Biomembranes 1858 (7), 1741-1752 (2016) [pdf]
    14. Matthes D, Gapsys V, Brennecke JT, de Groot BL. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci. Rep. 6, 33156 (2016) [pdf] [supplement]
    15. Schewe M, Nematian-Ardestani E, Sun H, Musinszki M, Cordeiro S, Bucci G, de Groot BL, Tucker SJ, Rapedius M, Baukrowitz T. A Non-Canonical Voltage Sensor Controls Gating in K2P K2 Channels. Cell. 164 (5), pp. 937-949 (2016) [pdf] [supplement] [pdf+supplement]
    16. Singer M, Krivobokova T, Munk A, de Groot BL. Partial least squares for dependent data. Biometr. 103 (2), pp. 351-362 (2016) [pdf] [supplement]
    17. Smith CA, Ban D, Pratihar, S, Giller K, Paulat M, Becker S, Griesinger C, Lee D, de Groot BL. Allosteric switch regulates protein–protein binding through collective motion. Proc. Nat. Acad. Sci. 113 (12), pp. 3269-3274 (2016) [pdf] [supplement]
    18. Voss B, Seifert R, Kaupp B, Grubmüller H. A Quantitative Model for cAMP Binding to the Binding Domain of MloK1. Biophys J. 111, 1668-1678 (2016) [pdf]
    19. Walczak M, Grubmuller H. BASDet: Bayesian approach(es) for structure determination from single molecule X-ray diffraction images. Comput. Phys. Comm. 201, pp. 159-166 (2016) [pdf]


    1. Andrini O, Keck M, Briones R, Lourdel S, Vargas-Poussou R, Teulon J. ClC-K chloride channels: Emerging pathophysiology of Bartter syndrome type 3. Am. J. Physiol - Renal Physiol. 308 (12), pp. F1324-F1334 (2015) [pdf]
    2. Bock LV, Blau C, Vaiana AC, Grubmüller H. Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation. Nucl. Acids Res. 43 (14), 6747–6760 (2015) [pdf] [supplement]
    3. Fischer N, Neumann P, Konevega AL, Bock LV, Ficner R, Rodnina MV, Stark H. Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 520, 567-570 (2015) [pdf+methods]
    4. Gapsys V, Michielssens S, Peters JH, de Groot BL, Leonov H. Calculation of binding free energies. Molecular modelling of proteins, Springer Protocols, book chapter 173-209 (2015) [pdf]
    5. Gapsys V, Michielssens S, Seeliger D, de Groot BL. Pmx: Automated protein structure and topology generation for alchemical perturbations. J. Comput. Chem. 36 (5), 348-354 (2015) [pdf]
    6. Gapsys V, Narayanan RL Xiang S de Groot BL, Zweckstetter M. Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. J. Biol. NMR 63 (3), pp. 299-307 (2015) [pdf]
    7. Halder K, Dölker N, Van Q, Gregor I, Dickmanns A, Baade I, Kehlenbach RH, Ficner R, Enderlein J, Grubmüller H, Neumann H. MD simulations and FRET reveal an environment: Sensitive conformational plasticity of Importin-beta. Biophys. J. 109 (2), pp. 277-286 (2015) [pdf] [supplement]
    8. Kaptan S, Assentoft M, Schneider HP, Fenton RA, Deitmer JW, MacAulay N, de Groot BL. H95 is a pH-dependent gate in aquaporin 4. Structure. 23 (12), pp. 2309-2318 (2015) [pdf] [supplement]
    9. Kumar R, Grubmüller H. do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations. Bioinf. 31 (15), 2583-2585 (2015) [pdf]
    10. Kutzner C, Páll S, Fechner M, Esztermann A, de Groot B, Grubmüller H. Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J. Comput. Chem. 36, 1990–2008 (2015) [pdf] [supplement]
    11. Linser R, Salvi N, Briones R, Rovo P, de Groot BL, Wagner G. The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proc. Nat. Acad. Sci. 112 (40), 12390–12395 (2015) [pdf] [supplement]
    12. Machtens JP, Kortzak D, Lansche C, Leinenweber A, Kilian P, Begemann B, Zachariae U, Ewers D, de Groot BL, Briones R, Fahlke C. Mechanisms of anion conduction by coupled glutamate transporters. Cell 160 (3), 542-553 (2015) [pdf] [supplement]
    13. Michielssens S, de Groot BL, Grubmüller H. Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations. Biophys. J. 108(10) 2585–2590 (2015) [pdf]
    14. Milovanovic D, Honigmann A, Koike S, Göttfert F, Pahler G, Junius M, Müller S, Diederichsen U, Janshoff A, Grubmüller H, Risselada HJ, Eggeling C, Hell SW, van den Bogaart G, Jahn R. Hydrophobic mismatch sorts SNARE proteins into distinct membrane domains. Nature Comm. 6, 5984 (2015) [pdf] [supplement]
    15. Osadnik H, Schöpfel M, Heidrich E, Mehner D, Lilie H, Parthier C, Risselada HJ, Grubmüller H, Brüser T, Stubbs MT. The PspF-binding domain PspA1-144 and the PspA·F complex - New insights into the coiled-coil dependent regulation of AAA+ proteins. Mol. Microbiol. 98(4), 743–759 (2015) [pdf] [supplement]
    16. Páll S, Abraham MJ, Kutzner C, Hess B, Lindahl E. Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS. Springer Int. Pub., book chapter, Switzerland 3–27 (2015) [pdf]
    17. Papadopoulos T, Schemm R, Grubmüller H, Brose N. Lipid binding defects and perturbed synaptogenic activity of a Collybistin R290H mutant that causes epilepsy and intellectual disability. J. Biol. Chem. 290 (13), 8256-8270 (2015) [pdf]
    18. Rauscher S, Gapsys V, Gajda MJ, Zweckstetter M, de Groot BL, Grubmuller H. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment. J. Chem. Theor. Comput. 11 (11), 5513-5524 (2015) [pdf]
    19. Rose AS, Ulrich Zachariae U, Grubmüller H, Hofmann KP, Scheerer P, Hildebrand PW. Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction. PLoS One. 10 (11), 1-13 (2015) [pdf] [supplement]
    20. Smith CA, Ban D, Pratihar S, Giller K, Schwiegk C, de Groot BL, Becker S, Griesinger C, Lee D. Population shuffling of protein conformations. Angew. Chem. 54 (1), 207-210 (2015) [pdf] [supplement]
    21. Taubert J, Hou B, Risselada, HJ, Mehner D, Lünsdorf H, Grubmüller H, Brüser T. TatBC-independent TatA/Tat substrate interactions contribute to transport efficiency. PLoS One 10(3), 1-24 (2015) [pdf]
    22. Wiederschein F, Vöhringer-Martinez E, Beinsen A, Postberg F, Schmidt J, Srama R, Stolz F, Grubmüller H, Abel B. Charge separation and isolation in strong water droplet impacts. PCCP 17 (10), 6858-6864 (2015) [pdf] [supplement]


  1. Czub J, Grubmüller H. Rotation triggers nucleotide-independent conformational transition of the empty beta subunit of F-1-ATPase. J. Am. Chem. Soc. 136 (10), 6960-6968 (2014) [pdf] [supplement]
  2. Graen T, Höfling M, Grubmüller H. AMBER-DYES: Characterization of charge fluctuations and force field parameterization of fluorescent dyes for molecular dynamics simulations. J. Chem. Theor. Comput. 10 (12), 5505-5512 (2014) [pdf]
  3. Hub JS, de Groot BL, Grubmüller H, Groenhof G. Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge. J. Chem. Theory Comput. 10 (1), 381-390 (2014) [pdf]
  4. Hub JS, Wolf MG, Caleman C, Maaren PJ, Groenhof G, van der Spoel D. Thermodynamics of hydronium and hydroxide surface solvation. Chem. Sci. 5 (5), 1745-1749 (2014) [pdf] [supplement]
  5. Köpfer DA, Song C, Gruene T, Sheldrick GM, Zachariae U, de Groot BL. Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 345 (6207), 352-355 (2014) [pdf] [supplement]
  6. Kumar R, Grubmüller H. Elastic Properties and Heterogeneous Stiffness of the Phi29 Motor Connector Channel. Biophys. J. 106, 1338-1348 (2014) [pdf] [supplement] [pdf+supplement]
  7. Kutzner C, Apostolov R, Hess B, Grubmüller H. Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. Parallel Computing: Accelerating Computational Science and Engineering (CSE) 722-730, IOS Press , NL, book chapter (2014) [pdf]
  8. Matthes D, Daebel V, Meyenberg K, Riedel D, Heim G, Diederichsen U, Lange A, de Groot BL Spontaneous aggregation of the insulin-derived steric zipper peptide VEALYL results in different aggregation forms with common features. J. Mol. Biol. 426 (2), 362-376 (2014) [pdf]
  9. Michielssens S, Peters JH, Ban D, Pratihar S, Seeliger D, Sharma M, Giller K, Sabo TM, Becker S, Lee D, Griesinger C, de Groot BL. A designed conformational shift to control protein binding specificity. Angew. Chem. 53 (39), 10367-10371 (2014) [pdf] [supplement]
  10. Risselada HJ, Bubnis G, Grubmüller H. Expansion of the fusion stalk and its implication for biological membrane fusion. Proc. Nat. Acad. Sci. 111 (30), 11043-11048 (2014) [pdf] [supplement]
  11. Risselada HJ, Smirnova Y, Grubmüller H. Free energy landscape of rim-pore expansion in membrane fusion. Biophys. J. 107 (10), 2287-2295 (2014) [pdf]
  12. Rose AS, Elgeti M, Zachariae U, Grubmüller H, Hofmann KP, Scheerer P, Hildebrand PW. Position of transmembrane Helix 6 determines receptor G protein coupling specificity. J. Am. Chem. Soc. 136 (32), 11244-11247 (2014) [pdf] [supplement]
  13. Vöhringer-Martinez E, Link O, Lugovoy E, Siefermann KR, Wiederschein F, Grubmüller H, Abel B. Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy. Phys. Chem. Chem. Phys. 16 (36), 19365-19375 (2014) [pdf]
  14. Walczak M, Grubmüller H. Bayesian orientation estimate and structure information from sparse single-molecule x-ray diffraction images. Phys. Rev. E 90 (2) (2014) [pdf]
  15. Wolf MG, Groenhof G Explicit proton transfer in classical molecular dynamics simulations. J. Comput. Chem. 35 (8), 657-671 (2014) [pdf]
  16. Wolf MG, Grubmüller H, Groenhof G. Anomalous surface diffusion of protons on lipid membranes. Biophys. J. 107 (1), 76-87 (2014) [pdf] [supplement]


  1. Assentoft M, Kaptan S, Fenton RA, Hua SZ, de Groot BL, MacAulay N. Phosphorylation of rat aquaporin-4 at Ser111 is not required for channel gating. Glia 61 (7), 1101-1112 (2013) [pdf]
  2. Bennett WFD, Chen AW, Donnini S, Groenhof G, Tieleman DP. Constant pH simulations with the coarse-grained MARTINI model - Application to oleic acid aggregates. Can.J.Chem. 91 (9), 839-846 (2013) [pdf]
  3. Blau C, Grubmüller H. g_contacts: Fast contact search in bio-molecular ensemble data. Comput. Phys. Comm. 184 (12), 2856-2859 (2013) [pdf]
  4. Bock LV, Blau C, Schröder GF, Davydov II, Fischer N, Stark H, Rodnina MV, Vaiana AC, Grubmüller H. Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Struct. Molec. Biol. 20 (12), 1390-1396 (2013) [pdf] [supplement]
  5. Brandani GB, Schor M, MacPhee CE, Grubmüller H, Zachariae U, Marenduzzo D. Quantifying disorder through conditional entropy: An application to fluid mixing. PLoS One 8 (6), e65617 (2013) [pdf]
  6. Dölker N, Blanchet CE, Voss B, Haselbach D, Kappel C, Monecke T, Svergun DI, Stark H, Ficner R, Zachariae U, Grubmüller H, Dickmanns A. Structural determinants and mechanism of mammalian CRM1 allostery. Structure 21 (8), 1350-1360 (2013) [pdf] [supplement]
  7. Gapsys V, de Groot BL, Briones R. Computational analysis of local membrane properties. J. Comput. Aided Mol. Des. 27 (10), 845-858 (2013) [pdf]
  8. Gapsys V, de Groot BL. Optimal superpositioning of flexible molecule ensemble. Biophys J. 104 (1), 196-207 (2013) [pdf] [supplement]
  9. Groenhof, G. Introduction to QM/MM simulations. Meth. Mol. Biol. 92 4, 43-66, book chapter (2013) [pdf]
  10. Hoefling M, Grubmüller H. In silico FRET from simulated dye dynamics. Comput. Phys. Comm. 184, 841-852 (2013) [pdf]
  11. Honigmann A, van den Bogaart G, Iraheta E, Risselada HJ, Milovanovic D, Müller V, Müller S, Diederichsen U, Fasshauer D, Grubmüller H, Hell SW, Eggeling C, Kühnel K, Jahn R. Phosphatidylinositol 4,5-bisphosphate clusters act as molecular beacons for vesicle recruitment. Nature Struct. Mol. Biol. 20 (6), 679-686 (2013) [pdf] [supplement]
  12. Inhester L, Groenhof G, Grubmüller H. Core hole screening and decay rates of double core ionized first row hydrides. J. Chem. Phys. 138 (16), 164304 (2013) [pdf] [errata]
  13. Li W, Edwards SA, Lu L, Kubar T, Patil SP, Grubmüller H, Groenhof G, Gräter F. Force distribution analysis of mechanochemically reactive dimethylcyclobutene. ChemPhysChem 14 (12), 2687-2697 (2013) [pdf] [supplement]
  14. Linder T, de Groot BL, Stary-Weinzinger A. Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Comput. Biol. 9 (2013) [pdf]
  15. Meyer T, Gabelica V, Grubmüller H. Orozco M. Proteins in the gas phase. Wiley Interdisc. Reviews: Comput. Mol. Sci. 3 (4), 408-425 (2013) [pdf]
  16. Monecke T, Haselbach D, Voß B, Russek A, Neuma P, Thomson E, Hurt E, Zachariae U, Stark H, Grubmüller H, Dickmanns A, Ficner R. Structural basis for cooperativity of CRM1 export complex formation. Proc. Nat. Acad. Sci. 110, 960-965 (2013) [pdf] [supplement]
  17. Paltrinieri L, Borsari M, Battistuzzi G, Sola M, Dennison C, de Groot BL, Corni S, Bortolotti CA. How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochem. 52 (42), 7397-7404 (2013) [pdf]
  18. Seeliger D, Zapater C, Krenc D, Haddoub R, Flitsch S, Beitz E, Cerdà J, De Groot BL. Discovery of novel human aquaporin-1 blockers. ACS Chem. Biol. 8 (1), 249-256 (2013) [pdf][supplement]
  19. Smirnova YG, Aeffner S, Risselada HJ, Salditt T, Marrink SJ, Müller M, Knecht V. Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter 9 (45), 10705-10718 (2013) [pdf] [supplement]
  20. Song C, Weichbrodt C, Salnikov E, Dynowski M, Forsberg B, Bechinger B, Steinem C, de Groot BL, Zachariae U, Zeth K. Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc. Nat. Acad. Sci. 110 (12), 4586-4591 (2013) [pdf][supplement]
  21. Vesper MD, de Groot BL. Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Comput. Biol. 9 (9) (2013) [pdf]
  22. Vukovic L, Burmeister CF, Kral P, Groenhof G. Control mechanisms of photoisomerization in protonated Schiff bases. J. Phys. Chem. Let. 4 (6), 1005-1011 (2013) [pdf] [supplement]
  23. Wacker S, Aponte-Santamaria C, Kjellbom P, Nielsen S, de Groot BL, Rützler M. The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Mol. Membr. Biol. 30 (3), 246-260 (2013) [pdf]
  24. Xiang SQ, Gapsys V, Kim HY, Bessonov S, Hsiao HH, Möhlmann S, Klaukien V, Ficner R, Becker S, Urlaub H, Lührmann R, de Groot B, Zweckstetter M. Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), 2162-2174 (2013) [pdf] [supplement]


  1. Aponte-Santamaria C, Briones R, Schenk AD, Walz T, de Groot BL. Molecular driving forces defining lipid positions around aquaporin-0. Proc. Nat. Acad. Sci. 109, 44319-44325 (2012) [pdf] [supplement]
  2. Beissner M, Dutertre S, Schemm R, Danker T, Sporning A, Grubmüller H, Nicke A. Efficient Binding of 4/7 α-conotoxins to Nicotinic α4β2 Receptors is Prevented by R185 and P195 in the α4 Subunit. Mol. Pharmacol. 82, 1–8 (2012)
  3. Boggio-Pasqua M, Burmeister C, Robb MA, Groenhof G. Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulation. Phys. Chem. Chem. Phys. 14, 7912-7928 (2012) [pdf]
  4. Buelens FP, Grubmüller H. Linear-scaling soft-core scheme for alchemical free energy calculations. J. Comput. Chem. 33, 25-33 (2012) [pdf]
  5. Gapsys V, Seeliger D, de Groot BL. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations. J. Chem. Theor. Comput. 8, 2373-2382 (2012) [pdf]
  6. Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmüller H. Exploring Protein Dynamics Space: The Dynasome as the Missing Link between Protein Structure and Function. PLoS One 7, e33931 (2012) [pdf]
  7. Inhester L, Burmeister CF, Groenhof G, Grubmüller H. Auger spectrum of a water molecule after single and double core ionization. J. Chem. Phys. 136, 144304 (2012) [pdf] [errata]
  8. Kappel C, Dölker N, Kumar R, Grubmüller H. Universal relaxation governs the nonequilibrium elasticity of biomolecules. Phys. Rev. Lett. 109, 118304 (2012) [pdf] [supplement]
  9. Köpfer DA, Hahn U, Ohmert I, Vriend G, Pongs O, de Groot BL, Zachariae U. A Molecular Switch Driving Inactivation in the Cardiac K+ Channel hERG. PLoS One. 7, e41023 (2012) [pdf]
  10. Krivobokova T, Briones R, Hub JS, Munk A, de Groot BL. Partial least squares functional mode analysis: application to the membrane proteins AQP1, Aqy1 and CLC-ec1. Biophys. J. 103, 786-796 (2012) [pdf]
  11. Matthes D, Gapsys V, de Groot BL. Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations. J. Mol. Biol. 421, 390-416 (2012) [pdf] [supplement]
  12. Michielssens S, van Erp TS, Kutzner C, Ceulemans A, de Groot BL. Molecular Dynamics in Principal Component Space. J. Phys. Chem. B 116, 8350-8354 (2012) [pdf]
  13. Peters JH, de Groot BL. Ubiquitin dynamics in complexes reveal molecular recognition mechanisms beyond induced fit and conformational selection. PLoS Comput. Biol. 8, e1002704 (2012) [pdf]
  14. Pool R, Heringa J, Hoefling M, Schulz R, Smith J, Feenstra K. Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS Through the GromPy Python Interface Module. J. Comput. Chem. 33, 1207-1214 (2012) [pdf]
  15. Portella G, Polupanow T, Zocher F, Boytsov DA, Pohl P, Diederichsen U, de Groot BL. Design of peptide-membrane interactions to modulate single-file water transport through modified gramicidin channels. Biophys. J. 103, 1698-1705 (2012) [pdf] [supplement]
  16. Risselada HJ, Grubmüller H. How SNARE molecules mediate membrane fusion: Recent insights from molecular simulations. Curr. Opin. Struct. Biol. 22, 187-196 (2012) [pdf]
  17. Risselada HJ, Marelli G, Fuhrmans M, Smirnova YG, Grubmüller H, Marrink SJ, Müller M. Line-Tension Controlled Mechanism for Influenza Fusion. PLoS One 7(6), e38302 (2012) [pdf]
  18. Seeliger D, Soeroes S, Klingberg R, Schwarzer D, Grubmüller H, Fischle W. Quantitative assessment of protein interaction with methyl-lysine analogues by hybrid computational and experimental approaches. ACS Chem Biol. 7, 150-154 (2012) [pdf] [supplement]
  19. Sieben C, Kappel C, Zhu R, Wozniak A, Rankl C, Hinterdorfer P, Grubmüller H, Herrmann A. Influenza virus binds its host cell using multiple dynamic interactions revealed by single-virus force spectroscopy and force-probe molecular dynamics. Proc. Nat. Acad. Sci. 109, 13626-13631 (2012) [pdf] [supplement]
  20. Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CWG, Johnson P, Madge D, Lindahl E, Rolland JF, de Groot BL. Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2(3) by High-Throughput Virtual Screening and Automated Patch Clamp. ChemMedChem 7, 1775-1783 (2012) [pdf] [supplement]
  21. Wolf M, Groenhof G. Evaluating non-polarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and water-chloroform partition coefficients. J. Comput. Chem. 33, 2225-2232 (2012) [pdf] [supplement]
  22. Zachariae U, Schneider R, Briones R, Gattin Z, Demers JP, Giller K, Maier E, Zweckstetter M, Griesinger C, Becker S, Benz R, de Groot BL, Lange A. Beta-barrel mobility underlies closure of the voltage-dependent anion channel. Structure 20, 1540-1549 (2012) [pdf] [supplement]


  1. Ban D, Funk M, Gulich R, Egger D, Sabo TM, Walter KFA , Fenwick RB, Giller K, Pichierri F, de Groot BL, Lange OF, Grubmüller H, Salvatella X, Wolf M, Loidl A, Kree R, Becker S, Lakomek NA, Lee D, Lunkenheimer P, Griesinger C. Kinetics of Conformational Sampling in Ubiquitin. Angew. Chem. 50, 11437-11440 (2011) [pdf]
  2. Boggio-Pasqua M, Groenhof G. Controlling the photoreactivity of the photoactive yellow protein chromophore by substituting at the p-coumaric acid group. J. Phys.Chem. 115, 7021-7028 (2011) [pdf]
  3. 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]
  4. Czub J and Grubmüller H. Torsional elasticity and energetics of F1-ATPase. Proc. Nat. Acad. Sci. 108; 7408-7413 (2011) [pdf]
  5. 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]
  6. 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]
  7. Donnini S, Tegeler F, Groenhof G, Grubmüller H. Constant pH Molecular Dynamics in Explicit Solvent with lambda-Dynamics. J. Chem. Theor. Comput. 7, 1962-1978 (2011) [pdf]
  8. 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]
  9. 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]
  10. Jelen S, Wacker S, Aponte-Santamaria C, Skott M, Rojek A, Johanson U, Kjellbom P, Nielsen S, de Groot BL, Rützler M. Aquaporin-9 Protein Is the Primary Route of Hepatocyte Glycerol Uptake for Glycerol Gluconeogenesis in Mice. J. Biol. Chem. 286, 44319-44325 (2011) [pdf] [supplement]
  11. Kappel C, Grubmüller H. Velocity dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network. Biophys. J. 100, 1109-1119 (2011) [pdf]
  12. Kutzner C, Czub J, and Grubmüller H. Keep it Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS. J. Chem. Theor. Comput. 7, 1381-1393 (2011) [pdf]
  13. 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]
  14. Lopez M, Vu H, Wang CK, Wolf MG, Groenhof G, Innocenti A, Supuran CT, Poulsen SA. Promiscuity of Carbonic Anhydrase II. Unexpected Ester Hydrolysis of Carbohydrate-Based Sulfamate Inhibitors. J. Am. Chem. Soc. 133, 18452-18462 (2011) [pdf] [supplement]
  15. 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]
  16. 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]
  17. 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]
  18. Seeliger D, Buelens FP, Goette M, de Groot BL, Grubmüller H. Towards computional specificity screening of DNA-binding proteins. Nucl. Acids Res. 39 (19), 8281–8290 (2011) [pdf] [supplement]
  19. 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] [supplement]
  20. Van den Bogaart G, Thutupalli S, Risselada HJ, Holt M, Riedel D, Herminghaus S, Grubmüller H, Jahn R. Synaptotagmin-1 may be a distance regulator acting upstream of SNARE nucleation? Nature Struct. Mol.Biol. 18, 805-812 (2011) [pdf]


    1. 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]
    2. 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]
    3. 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. J. Biol. Chem. 285, 14603-14609 (2010) [pdf]
    4. 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]
    5. Dölker N, Zachariae U, and Grubmüller H. Hydrophilic Linkers and Polar Contacts Affect Aggregation of FG Repeat Peptides. Biophys. J. 98, 2653-2661 (2010) [pdf]
    6. 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]
    7. 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] [supplement]
    8. Groenhof G, Boggio-Pasqua M, and Robb MA. Computer Simulations of Photobiological Processes: the effect of the protein environment. Advanc. in Quant. Chem. 59, 181-212, book chapter (2010) [pdf]
    9. Hensen U, Lange OF, Grubmüller H. Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach. PLoS One 5, e9179 (2010) [pdf]
    10. Hub JS, Aponte-Santamaria C, Grubmüller H, and de Groot BL. Voltage-Regulated Water Flux through Aquaporin Channels in Silico. Biophys. J. 99, L97-L99 (2010) [pdf] [supplement]
    11. Hub JS, de Groot BL, and van der Spoel D. g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates. J. Chem. Theory Comput. 6, 3713-3720 (2010) [pdf]
    12. 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]
    13. 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]
    14. 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] [supplement]
    15. 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] [support]
    16. 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]
    17. Nunes JM, Hensen U, Ge L, Lipinsky M, Helenius J, Grubmüller H, and Müller DJA. A "Force Buffer" Protecting Immunoglobin Titin. Angew. Chem. 49, 3528-3531 (2010) [pdf]
    18. Seeliger D and de Groot BL. Conformational transitions upon ligand binding: Holo structure prediction from apo conformations. PLoS Comput. Biol. 6, e1000634 (2010) [pdf]
    19. Seeliger D and de Groot BL. Ligand docking and binding site analysis with PyMOL and Autodock/Vina. J. Comput. Aided Mol. Des. 24, 417-422 (2010) [pdf]
    20. Seeliger D and de Groot BL. Protein thermostability calculations using alchemical free energy simulations. Biophys. J. 98, 2309-2316 (2010) [pdf] [support]
    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. 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] [support]
    23. 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]
    24. 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. Comput. Chem. 31, 2169-2174 (2010) [pdf]
    25. 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]


  1. Benedix A, Becker CM, de Groot BL, Caflisch A, Böckmann RA. Predicting Free Energy Changes Using Structural Ensembles. Nature Meth. 6, 3-4 (2009) [pdf]
  2. Boggio-Pasqua M, Robb MA, Groenhof G. Hydrogen bonding controls excited-state decay of the photoactive yellow protein chromophore. J. Am. Chem. Soc. 131, 13581-13581 (2009) [pdf]
  3. Donnini S, Villa A, Groenhof G, Mark AE, Wierenga RK, Juffer AH. Inclusion of ionization states of ligands in affinity calculations. Proteins 76, 138-150 (2009) [pdf]
  4. 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]
  5. Goette M, Grubmüller H. Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. J. Comput. Chem. 30, 447-456 (2009) [pdf]
  6. 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]
  7. Groenhof G, Schaefer LV, Boggio-Pasqua M, Robb MA. Excited state dynamics in biomolecules. Handb. Mol. Biophys., Ed. H.Bohr Wiley, New York, book chapter (2009)
  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. Hensen U, Grubmüller H, Lange OF. Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. Phys. Rev. E. 80, 011913 (2009) [pdf]
  10. Hub JS, de Groot BL. Detection of functional modes in protein dynamics. PLoS Comput. Biol. 5, e1000480 (2009) [pdf]
  11. 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, book chapter (2009) [pdf]
  12. Joshi HV, Jedrzejas MJ, de Groot BL. Domain motions of hyaluronan lyase underlying processive hyaluronan translocation. Proteins 76, 30-46 (2009) [pdf]
  13. 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. Cell Sci. 122, 3759-3771 (2009) [pdf]
  14. Kubitzki MB, de Groot BL, Seeliger D. Protein dynamics: from structure to function. From Protein Struct. to Func. with Bioinf. pp. 217-249, book chapter (2009) [pdf]
  15. 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 Disc. 141, 67-79 (2009) [pdf]
  16. 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]
  17. Portella G, de Groot, BL. Determinants of water permeability through nanoscopic hydrophilic channels. Biophys. J. 96, 925-938 (2009) [pdf] [new & notable pdf]
  18. Reinhard F, Lange OF, Hub JS, Haas J, Grubmüller H. g_permute: Permutation-reduced phase space density compaction. Comput. Phys. Comm. 180, 455-458 (2009) [pdf]
  19. Seeliger D, de Groot, BL. tCONCOORD-GUI: Visually Supported Conformational Sampling of Bioactive Molecules. J. Comput. Chem. 30, 1160-1166 (2009) [pdf]
  20. Stegmann CM, Seeliger D, Sheldrick GM, de Groot BL, Wahl M. Thermodynamic influence of trapped water molecules in a protein-ligand interaction. Angew. Chem. 48, 5207-5210 (2009) [pdf]
  21. Stumpe MC, Grubmüller H. Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophys. J. 96, 3744 - 3752 (2009) [pdf]
  22. Zink M, Grubmüller H. Mechanical properties of the icosahedral shell of southern bean mosaic virus: a molecular dynamics study. Biophys. J. 96, 1350-1363 (2009) [pdf]
  23. Zink M, Grubmüller H. Simulation of a Complete Viral Shell. InSiDE 7, 22-25 (2009) [pdf]


    1. Böckmann RA, de Groot BL, Kakorin S, Neumann E, Grubmüller H. Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations. Biophys. J. 95, 1837-1850 (2008) [pdf]
    2. Fabiano E, Groenhof G, Thiel W. Approximate switching algorithms for trajectory surface hopping. Chem. Phys. 351, 111-116 (2008) [pdf]
    3. Groenhof G, Schäfer LV, Boggio-Pasqua M, Grubmüller H, Robb MA. Arginine52 controls the photoisomerization process in Photoactive Yellow Protein. J. Am. Chem. Soc. 130, 3250-3251 (2008) [pdf]
    4. Grubmüller H. Editorial: Wunderwerke der Evolution. Phys. in uns. Zeit 1/08, 3 (2008) [pdf]
    5. 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]
    6. Hayward S, de Groot BL. Normal modes and essential dynamics. Molecular modelling of proteins , book chapter (2008)
    7. 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]
    8. Hub JS, de Groot BL. Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc. Nat. Acad. Sci. 105, 1198-1203 (2008) [pdf]
    9. Klyszejko AL, Shastri S, Mari SA, Grubmüller H, Muller DJ, Glaubitz C. Folding and Assembly of Proteorhodopsin. J. Mol. Biol. 376, 35-41 (2008) [pdf]
    10. 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]
    11. 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, 1433-1437 (2008) [pdf]
    12. Lakomek NA, Walter KFA, Farès C, Lange OF, de Groot BL, Grubmüller 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]
    13. Lange OF, Grubmüller H. Full Correlation Analysis of Conformational Protein Dynamics. Proteins 70, 1294-1312 (2008) [pdf]
    14. Lange OF, Lakomek NA, Farès C, Schröder GF, Walter KFA, Becker S, Meiler J, Grubmüller 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. Müller EM, Hub JS, Grubmüller H, de Groot BL. Is TEA an inhibitor for human Aquaporin-1? Pflugers Arch - Eur. J. Physiol. (2008) [pdf]
    16. Nagendran S, Sen SS, Roesky HW, Koley D, Grubmüller 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, 5459-5463 (2008) [pdf]
    17. 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]
    18. Puchner EM, Alexandrovich A, Kho AL, Hensen U, Schäfer LV, Brandmeier B, Gräter F, Grubmüller H, Gaub HE, Gautel M. Mechanoenzymatics of titin kinase. Proc. Nat. Acad. Sci. 105, 13385-13390 (2008) [pdf]
    19. Schäfer LV, Groenhof G, Boggio-Pasqua M, Robb M, Grubmüller H. Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595. PLoS Comput. Biol. 4, e1000034 (2008) [pdf]
    20. Stumpe MC, Grubmüller H. Polar or apolar - the role of polarity for urea-induced protein denaturation. PLoS. Comput. Biol. 4, e1000221 (2008) [pdf]
    21. Wozniak AK, Schröder GF, Grubmüller H, Seidel CA, Oesterhelt F. Single-molecule FRET measures bends and kinks in DNA. Proc. Natl. Acad. Sci. 105, 18337-18342 (2008) [pdf]
    22. 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]
    23. Zachariae U, Grubmüller H. Importin-ß: Structural and Dynamic Determinants of a Molecular Spring. Structure 16, 906-915 (2008) [pdf]


  1. 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]
  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. Gräter F, Grubmüller H. Fluctuations of primary ubiquitin folding intermediates in a force clamp. J. Struct. Biol. 157, 557-569 (2007) [pdf]
  4. 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]
  5. Grubmüller H, Schulten K. Editorial: Advances in molecular dynamics simulations. J. Struct. Biol. 157 (3), 443-443 (2007)
  6. 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]
  7. Kubitzki MB, de Groot BL. Molecular Dynamics Simulations using Temperature Enhanced Essential dynamics Replica Exchange (TEE-REX). Biophys. J. 92, 4262-4270 (2007) [pdf]
  8. 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. Comput. Chem. 28, 2075-2084 (2007) [pdf]
  9. 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]
  10. Reinhard F, Grubmüller H. Estimation of absolute solvent and solvation shell entropies via permutation reduction. J. Chem. Phys. 126, 014102 (2007) [pdf]
  11. Schäfer LV, Müller EM, Gaub HE, Grubmüller H. Elastic properties of photoswitchable azobenzene polymers from molecular dynamics simulations. Angew. Chem. 46, 2232-2237 (2007) [pdf] [supporting info]
  12. 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. Chem. 119, 536-542 (2007) [pdf]
  13. 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]
  14. Seeliger D, Haas J, de Groot BL. Geometry-based Sampling of Conformational Transitions in Proteins. Structure 15, 1482-1492 (2007) [pdf]
  15. 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]
  16. Stumpe MC, Grubmüller H. Aqueous urea solutions: Structure, energetics, and urea aggregation. J. Phys. Chem. B 111, 6220-6228 (2007) [pdf]
  17. 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]
  18. 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]


  1. de Groot BL, Böckmann RA, Grubmüller H. Proteindynamik-Simulationen. Molekulare Nanomaschinen unter der Lupe. Phys. in uns. Zeit 37, 73-79 (2006) [pdf] [cover]
  2. 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. J. Biol. Chem. 281, 14207-14214 (2006) [pdf]
  3. Donnini S, Groenhof G, Wierenga RK, Juffer AH. The planar conformation of a strained proline ring: A QM/MM study. Proteins 64 (3), pp. 700-710 (2006) [pdf]
  4. 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]
  5. Gräter F, Xu W, Leal W, Grubmüller H. Pheromone Discrimination by the Pheromone-Binding Protein of Bombyx mori. Structure 14, 1577-1586 (2006) [pdf]
  6. 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, book chapter (2006)
  7. Hub JS, de Groot BL. Does CO2 permeate through Aquaporin-1? Biophys. J. 91, 842-848 (2006) [pdf]
  8. 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, Proceedings Series: Lecture Notes in Computer Science, B. Mohr, J. L. Träff, J. Worringen, J. Dongarra (Eds.) 404-405, book chapter (2006) [pdf]
  9. 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]
  10. Lange OF, Grubmüller H. Collective Langevin dynamics of conformational motions in proteins. J. Chem. Phys. 124, 214903 (2006) [pdf]
  11. Lange OF, Schäfer LV, Grubmüller H. Flooding in GROMACS: Accelerated Barrier Crossings in Molecular Dynamics. J. Comput. Chem. 27, 1693-1702 (2006) [pdf]
  12. Lange OF, Grubmüller H. Generalized Correlation for Biomolecular Dynamics. Proteins 62, 1053-1061 (2006) [pdf]
  13. 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]
  14. 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]
  15. Seeliger D, de Groot BL. Prediction of protein flexibility from geometrical constraints. Biotech Int. 18, 20-22 (2006) [pdf]
  16. 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]
  17. Stock G, Wachtveitl J, Grubmüller H. Editorial: Nonequilibrium dynamics in biomolecules. Chem Phys. 323, 1 (2006) [pdf]
  18. 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]
  19. Zachariae U, Grubmüller H. A Highly Strained Nuclear Conformation of the Exportin Cse1p Revealed by Molecular Dynamics Simulations. Structure 14, 1469-1478 (2006) [pdf]
  20. 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]


  1. 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]
  2. 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. Proc. Nat. Acad. Sci. 102, 13070-13074 (2005) [pdf]
  3. 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]
  4. 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]
  5. Grubmüller H. Force probe molecular dynamics simulations. In U. Nienhaus, Editor Protein-Ligand Interactions p. 493-515, Totowa, NJ, USA. The Humana Press Inc., book chapter (2005)
  6. 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]
  7. Kukulski W, Schenk AD, Johanson U, Braun T, de Groot BL, Fotiadis D, Kjellbom P, Engel A. The 5 angstrom structure of heterologously expressed plant Aquaporin SoPIP2;1. J. Mol. Biol. 350, 611-616 (2005) [pdf]
  8. Lange OF, Grubmüller H, de Groot BL. Molecular Dynamics Simulations of Protein G Challenge NMR-Derived Correlated Backbone Motions. Angew. Chem. 44, 3394-3399 (2005) [pdf]
  9. 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. Mol. Biol. Cell 16, 5675-5685 (2005) [pdf]
  10. Schenk AD, Werten PJL, Scheuring S, de Groot BL, Müller SA, Stahlberg H, Philippsen A, Engel A. The 4.5 angstrom structure of human AQP2. J. Mol. Biol. 350, 278-289 (2005) [pdf]
  11. Schröder GF, Alexiev U, Grubmüller H. Simulation of Fluorescence Anisotropy Experiments: Probing Protein Dynamics. Biophys. J. 89, 3757-3770 (2005) [pdf] [cover]
  12. 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]


  1. Böckmann RA, Grubmüller H. Multistep Binding of Divalent Cations to Phospholipid Bilayers: A Molecular Dynamics Study. Angew. Chem. 43, 1021-1024 (2004) [pdf] [german] [cover]
  2. de Groot BL, Grubmüller H. Aquaporine: Die perfekten Wasserfilter der Zelle. BIOspektrum 4, 384-386 (2004) [pdf]
  3. 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. Int.Ed. 53, 947-959 (2004) [pdf] [russian]
  4. 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. Forschungszentrum Jülich, book chapter (2004)
  5. 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. ChemPhysChem 5, 1150-1158 (2004) [pdf]
  6. 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]
  7. Schröder GF, Grubmüller H. FRETsg: Biomolecular structure model building from multiple FRET experiments. Comput. Phys. Comm. 158, 150-157 (2004) [pdf]


  1. Böckmann RA, Grubmüller H. Conformational dynamics of the F1-ATPase ß-subunit: A molecular dynamics study. Biophys. J. 85, 1482-1491 (2003) [pdf] [cover]
  2. Böckmann RA, Hac A, Heimburg T, Grubmüller H. Effect of sodium chloride on a lipid bilayer. Biophys. J. 85, 1647-1655 (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. 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]
  5. 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]
  6. 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]
  7. 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. Proc. Nat. Acad. Sci. 100, 15516-15521 (2003) [pdf] [supplement]
  8. Schröder GF, Grubmüller H. Maximum likelihood trajectories from single molecule fluorescence resonance energy transfer experiments. J. Chem. Phys. 119, 9920-9924 (2003) [pdf]


  1. 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]
  2. 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]
  3. de Groot BL, Grubmueller H. Aquaporine - Wasserfilter der Zelle. Bioforum 6, pp. 387-389 (2002)
  4. de Groot BL, Grubmueller H. Proteine als Filter reinsten Wassers. Max Planck Forschung 1, pp. 8-9 (2002)
  5. 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]
  6. Grubmueller H. Mechanik molekularer "Maschinen" am Beispiel des Aquaporins und der F1-ATPase. Jahrbuch der Max-Planck-Gesellschaft. pp. 121-125 (2002)
  7. Jahn R, Grubmüller H. Membrane fusion. Curr. Opin. Cell Biol. 14, 488-495 (2002) [pdf]
  8. 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]
  9. Lange O, Schroers BJ. Unstable manifolds and Schrodinger dynamics of Ginzburg-Landau vortices. Nonlinearity 15 (5), pp. 1471-1488 (2002)
  10. Margittai M, Schweinberger E, Widengren J, Fasshauer D, Jahn R, Schröder G, Grubmueller H, Haustein E, Felekyan S, Koenig M, Seidel C. Single molecule FRET reveals an equilibrium between a closed and an open conformation of syntaxin 1. Biophys. J. 82 (1), p. 305a-305a (2002)
  11. 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]
  12. Müller EM, de Meijere A, Grubmüller H. Predicting unimolecular chemical reactions: Chemical flooding. J. Chem. Phys. 116, 897-905 (2002) [pdf]
  13. Rief M, Grubmüller H. Force spectroscopy of single biomolecules. ChemPhysChem 3, 255-261 (2002) [pdf] [cover]
  14. 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]


  1. de Groot BL, Engel A, Grubmüller H. A refined structure of human Aquaporin 1. FEBS Lett. 504, 206-211 (2001) [pdf]
  2. 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. Mol. Biol. 309, 299-313 (2001) [pdf]
  3. de Groot BL, Grubmüller H. Water permeation across biological membranes: Mechanism and dynamics of Aquaporin-1 and GlpF. Science 294, 2353-2357 (2001) [pdf]
  4. 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]
  5. Rief M, Grubmüller H. Kraftspektroskopie von einzelnen Biomolekülen. Phys. Blätter 57 (2), 55-61 (2001) [pdf]


  1. de Groot BL, Heymann JB, Engel A, Mitsuoka K, Fujiyoshi Y, Grubmüller H. The fold of human Aquaporin 1. J. Mol. Biol. 300, 987-994 (2000) [pdf]
  2. 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. Structure 8(6), 643-653 (2000) [pdf]
  3. Heymann B, Grubmüller H. Dynamic force spectroscopy of molecular adhesion bonds. Phys. Rev. Lett. 84, 6126-6129 (2000) [pdf] [postscript]
  4. 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]
  5. 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]
  6. 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]


  1. de Groot BL, Vriend G, Berendsen HJC. Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism. J. Mol. Biol. 286 (4), pp. 1241-1249 (1999) [pdf]
  2. 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 397-402, World Scientific, Singapore 912805, book chapter (1999)
  3. Grubmüller H, Heymann B. Proteindynamik von Ligand/Rezeptor-Bindungen. MPIbpc news, Max-Planck-Institut für biophysikalische Chemie, Göttingen (1999) [pdf]
  4. Heymann B, Grubmüller H. AN02/DNP unbinding forces studied by molecular dynamics AFM simulations. Chem. Phys. Lett. 303, 1-9 (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. Elastic properties of poly(ethylene-glycol) studied by molecular dynamics stretching simulations. Chem. Phys. Lett. 307, 425-432 (1999) [pdf]
  7. 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 Simplicity and Complexity in Proteins and Nucleic Acids, Dahlem Workshop Reports 255-280, Dahlem University Press, Berlin, book chapter (1999)


  1. 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. Computational Molecular Dynamics: Challenges, Methods, Ideas 78-97, Springer, book chapter (1998) [pdf]
  2. Grubmüller H, Tavan P. Multiple time step algorithms for molecular dynamics simulations of proteins: How good are they? J. Comput. Chem. 19, 1534-1552 (1998) [pdf]


  1. Eichinger M, Grubmüller H, Heller H, Tavan P. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations. J. Comput. Chem. 18, 1729-1749 (1997) [pdf] [postscript] [html]
  2. 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' , pages III 45-50, Fondation Fourmentin-Guilbert, 93160 Noisy Le Grand, France (1997)
  3. Grubmüller H, Heymann B, Tavan P. Simulation eines molekularen Erkennungsvorgangs. Spektrum der Wissenschaft 14-16, März (1997)
  4. van Aalten DMF, de Groot BL, Berendsen HJC, Findlay JBC, Amadei A. A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem. 18 (2), pp. 169-181 (1997) [pdf]


  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]


  1. 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., Düsseldorf, Germany, June (1995)
  2. Eichinger M, Grubmüller H, Heller H. User Manual for EGO_VIII, Release 2.0. Lecture (1995) [html]
  3. Grubmüller H. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys. Rev. E. 52, 2893-2906 (1995) [pdf] [postscript] [html]


  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, Tavan P. Molecular dynamics of conformational substates for a simplified protein model. J. Chem. Phys. 101, 5047-5057 (1994) [pdf] [postscript] [html]
  3. Grubmüller H. Molekulardynamik von Proteinen auf langen Zeitskalen. PhD thesis, Technische Universität München, Jan (1994) [pdf] [postscript]
  4. Grubmüller H. Proteine: Einblicke in ihre Funktionsweise. 'Spektrum Videothek' , Heidelberg, Germany, Lecture (1994)


  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. J. Mol. Graph. 11, 258 (1993)


    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)


    1. Grubmüller H, Heller H, Windemuth A, Schulten K. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Mol. Simul. 6, 121-142 (1991) [pdf]
    2. 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, book chapter (1991)


    1. 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) [pdf]
    2. Heller H, Grubmüller H, Schulten K. Molecular dynamics simulation on a parallel computer. Mol. Simul. 5: 133-165 (1990) [pdf]
    3. 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) [pdf]


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

PhD theses at the department

  1. Timo Graen Coupling of Quantum and Classical Degrees of Freedom in Protein Simulations. PhD thesis, Physics, 2015
  2. Shreyas Kaptan Regulation of permeation in aquaporins PhD thesis, 2015 [pdf]
  3. David Köpfer Ion conductance through potassium channels. PhD thesis, 2015
  4. Bela Voß Conformational changes in ligand binding processes PhD thesis, Biophysics, 2014 [pdf]
  5. Michal Walczak Bayesian structure reconstruction from single molecule X-ray scattering data PhD thesis, Physics, 2014 [pdf]
  6. Rajendra Kumar Molecular Dynamics Studies of the Phi29 Connector-DNA complex PhD thesis, Biophysics, 2014 [pdf]
  7. Maike Clemens Influence of the Chromophore-Protein-Interaction on the chromophore isomerisation in Photoactive Yellow Protein PhD thesis, Chemistry, 2014 [pdf]
  8. Christian Blau Transfer RNA translocation through the ribosome. Combining large scale system simulations with experimental data PhD thesis, Physics, 2013 [pdf]
  9. Vytautas Gapsys Free Energy Calculations for Protein-Ligand Complexes and Intrinsically Disordered Peptides and Their Aggregates PhD thesis, Physics, 2013
  10. Jan Henning Peters On the Effect of Binding on Ubiquitin Dynamics PhD thesis, Physics, 2013 [pdf]
  11. Ludger Inhester Auger decay in double core ionized molecules PhD thesis, Physics, 2013 [pdf]
  12. Carl Burmeister Primary Effects of X-ray and Photo-Absorption Induced Excitations in Biomolecules PhD thesis, Physics, 2013 [pdf]
  13. Martin Vesper Collective Dynamics in Allosteric Transitions: A Molecular Dynamics Study PhD thesis, Physics, 2012 [pdf]
  14. Lars Bock Dynamics and Driving Forces of Macromolecular Complexes PhD thesis, Physics, 2012 [pdf]
  15. Sarath Dantu Conformational Sampling of Enzyme Dynamics: Triosephosphate Isomerase PhD thesis, Biology, 2012 [pdf]
  16. Sören Wacker Computer-Aided Drug Design for Membrane Channel Proteins PhD thesis, Physics, 2012 [pdf]
  17. Plamen Dobrev Protonation patterns in reduced and oxidized form of electron transfer proteins PhD thesis, Physics, 2012 [pdf]
  18. Dirk Matthes Spontaneous aggregation of fibril-forming peptides studied by Molecular Dynamics simulations PhD thesis, Chemics, 2011 [pdf]
  19. Martin Höfling Simulations and Experiments: How close can we get? PhD thesis, Physics, 2011 [pdf]
  20. Christian Kappel Structure and Dynamics of Proteins under Force PhD thesis, Physics, 2011 [pdf]
  21. Stephanus Fengler Estimating Orientational Water Entropy At Protein Interfaces. PhD thesis, Physics, 2011 [pdf]
  22. Camilo Aponte-Santamaria Understanding the molecular machinery of aquaporins through molecular dynamics simulations. PhD thesis, Physics, 2011 [pdf]
  23. Frank Wiederschein Investigation of Laser-Induced-Liquid-Beam-Ion-Desorption (LILBID) with Molecular Dynamics Simulations. PhD thesis, Physics, 2010 [pdf]
  24. Mareike Zink Mechanical Properties of Icosahedral Viral Shells. A Molecular Dynamics Study. PhD thesis, Physics, 2009 [pdf]
  25. Ulf Hensen Thermodynamic Driving Forces in Protein Regulation Studied by Molecular Dynamics Simulations. PhD thesis, Chemistry, 2009 [pdf]
  26. Maik Götte Free energy calculations of protein-ligand complexes with computational molecular dynamics. PhD thesis, Biology, 2008 [pdf]
  27. Esteban Vöhringer-Martinez Dynamics, ionization and charge separation in superheated metastable water. PhD thesis, Chemistry, 2008 [pdf]
  28. Guillem Portella Determinants of water and ion permeation through nanopores studied by Molecular Dynamics simulations. PhD thesis, Chemistry, 2008 [pdf]
  29. Daniel Seeliger Geometry-based Conformational Sampling of Proteins. PhD thesis, Chemistry, 2008 [pdf]
  30. Jochen Hub Selectivity, Regulation, and Inhibition of Aquaporin Channels. A Molecular Dynamics Study. PhD thesis, Physics, 2008 [pdf]
  31. Marcus Kubitzki Enhanced Conformational Sampling of Proteins Using TEE-REX. PhD thesis, Physics, 2007 [pdf]
  32. Martin Stumpe De natura denaturantium - On the molecular basis of urea-induced protein denaturation. PhD thesis, Physics, 2007 [pdf]
  33. Lars Schäfer Photoactivated Processes in condensed Phase studied by Molecular Dynamics Simulations. PhD thesis, Chemistry, 2007 [pdf]
  34. Harshad Joshi Functional Domain Motions and Processivity in Bacterial Hyaluronate Lyase: A Molecular Dynamics Study. PhD thesis, Physics, 2007 [pdf]
  35. Oliver Lange Collective Langevin Dynamics of Conformational Motions in Protein PhD thesis, Physics, 2005 published with Cuvillier Verlag [pdf]
  36. Frauke Gräter Enforced functional protein motions studied by Molecular Dynamic. PhD thesis, Chemistry , 2005 [pdf]
  37. Gunnar Schröder Simulation of Fluorescence Spectroscopy Experiments. PhD thesis, Physics, 2004 [pdf]
  38. Volker Knecht Membrane Fusion SNARE Protein Syntaxin-1A: A Molecular Dynamics Study. PhD thesis, Physics; Mensch und Buch Verlag, Berlin 2003 [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. Helmut Grubmüller Theorie und Simulation induzierter Konformationsdynamik von Proteinen postdoctoral lecture qualification (Habilitation) Physics, 2001 [pdf]
  42. Berthold Heymann Molekulardynamiksimulationen kraftmikroskopischer Einzelmolekülexperimente. PhD thesis, Physics, 2000 [pdf]

Diploma/Master/Bachelor theses at the department

  1. Daniel Quetschlich Markov State Models for Comparing Protein Dynamics Master thesis, Physics, 2016
  2. Julian Tim Brennecke Allosteric Transitions. Master thesis, Physics, 2014
  3. Max Linke Analysis of protein dynamics with Markov models. Master thesis, Physics, 2014 [pdf]
  4. Bartosz Guzek Untersuchung des antimikrobellen Effekts von Dermcidin mithilfe von Computersimulationen. Bachelor thesis, Physics, 2014 [pdf]
  5. Andreas Volkhardt Analysing Anomalous Diffusion Processes on Hierarchical Energy Landscapes With Time Scale Dependent Principal Component Analysis. Master thesis, Physics, 2013
  6. Terence Thias Comparison of Particle mesh Ewald Method with Fast Mulitpole Method Bachelor thesis, Physics, 2013
  7. Benjamin von Ardenne Rekonstruktion von Elektronendichten aus Rötgenstreuexperimenten an einzelnen Molekülen bei geringer Photonenzahl Master thesis, Physics, 2013
  8. Julian Tim Brennecke Inhibition of peptide aggregation. Bachelor thesis, Physics, 2013 [pdf]
  9. Cornelius Müthel Calculation of Peptide Persistence Length from Molecular Dynamics Simulations Bachelor thesis, Physics, 2012 [pdf]
  10. Andreas Russek Simulation von Nucleoporin-Netzwerken Diploma thesis, Physics, 2011 [pdf]
  11. Fabian Knoch Steering excited state dynamics of biological chromophores by external electric fields. Bachelor thesis, Physics, 2011 [pdf]
  12. Timo Graen Anharmonic Infrared Spectra from Short QM/MM Simulations. Master thesis, Physics, 2011 [pdf]
  13. Béla Voß The Ligand Binding Mechanism of the MloK1 Ion Channel. Diploma thesis, Physics, 2010 [pdf]
  14. Michal Walczak Bayesian orientation estimate from single molecule x-ray scattering data. Diploma thesis, Physics, 2010 [pdf]
  15. David Köpfer Struktur-Aktivitätsbeziehungen in Membranproteinen: Berechnung von Blockeraktivitäten in hERG-Ionenkanälen. Diploma thesis, Physics, 2010
  16. Carl Friedrich Burmeister Interaction of Short X-ray Pulses with Biomolecules. Diploma thesis, Physics, 2009 [pdf]
  17. Christian Blau Effect of posttranscriptional modifications and Mg2+ ions on tRNA structure and flexibility. Diploma thesis, Physics, 2009 [pdf]
  18. Timo Graen Dye'ing for FRET: The HTH motif in smFRET-MD Simulation. Bachelor thesis, Physics, 2009 [pdf]
  19. René Rex Quantification of structure/dynamics correlation of globular proteins. Master thesis, Appl. Inform., 2009 [pdf]
  20. Sören Wacker Molecular Dynamics Study of Potassium Channels, their Interaction with Non-Amino Acid Compounds and Peptidic Scorpion Toxins. Diploma thesis, Physics, 2008 [pdf]
  21. Martin Vesper Verfeinerung der Proteinkristallographie durch Flexibilitätsvorhersagen. Diploma thesis, Physics, 2008 [pdf]
  22. Florian Tegeler Dynamic Protonation of Titrable Groups in Biomolecules for Molecular Dynamics Simulations. Diploma thesis, Physics, 2008 [pdf]
  23. Lars Bock Molecular Dynamics Simulations of the Nascent Peptide Chain in the Ribosomal Exit Tunnel. Diploma thesis, Physics, 2007 [pdf]
  24. Marcus Hennig Entropy-Preserving Transformation Method. Diploma thesis, Physics , 2007 [pdf]
  25. Florian Dommert The Unfolding Pathway of Ubiquitin in various chemical environments. Diploma thesis, Physics, 2007 [pdf]
  26. Christian Kappel Enforced Unfolding of Bacteriorhodopsin via Force Probe Molecular Dynamics. Diploma thesis, Physics, 2007 [pdf]
  27. Martin Meling Modellierung und Strukturanalyse von b-Faltblattkristalliten in Spinnenseide Diploma thesis, Physics, 2006 [pdf]
  28. Friedemann Reinhard Computation of solvent entropies from molecular dynamics simulations. Diploma thesis, Physics, 2005 [pdf]
  29. Jr-hung Lin Untersuchung der dielektrischen Relaxation von Wasser durch Molekulardynamiksimulation. Diploma thesis, Physics, 2002 [pdf]
  30. Gunnar Schröder Molekulardynamiksimulation der Flexibilität und Fluoreszenzanisotropie eines an ein Protein gebundenen Farbstoffs. Diploma thesis, Physics, 2001 [pdf]
  31. Helmut Grubmüller Dynamiksimulation sehr großer Makromoleküle auf einem Parallelrechner. Diploma thesis, Physics, Technische Universität München, 1989

Sep 07, 2017

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