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Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation.
Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G. J Proc Natl Acad Sci., 2020 [10.1073/pnas.1922488117]
Regulation of lipid saturation without sensing membrane fluidity.
Ballweg S, Sezgin E, Doktorova M, Covino R, Reinhard J, Wunnicke D, Hänelt I, Levental I, Hummer G, Ernst R.Nat Commun., 2020 [10.1038/s41467-020-14528-1]
Ion Binding and Selectivity of the Na+/H+ Antiporter MjNhaP1 from Experiment and Simulation.
Warnau J, Wöhlert D, Okazaki KI, Yildiz Ö, Gamiz-Hernandez AP, Kaila VRI, Kühlbrandt W, Hummer G. J Phys Chem B., 2020 [10.1038/s41467-020-14528-1]
Pietrek LM, Stelzl LS, Hummer G. J Chem Theory Comput., 2020 [10.1021/acs.jctc.9b00809]
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN Jr, et al. Structure., 2019 [10.1016/j.str.2019.11.002]
High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label.
Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G. Nucleic Acids Res., 2019 [10.1093/nar/gkz1096]
Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.
Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Mol Cell., 2019 [10.1016/j.molcel.2019.10.019]
Herhaus L, Bhaskara RM, Lystad AH, Gestal-Mato U, Covarrubias-Pinto A, Bonn F, Simonsen A, Hummer G, Dikic I. EMBO Rep., 2019 [10.15252/embr.201948317]
Covino R, Woodside MT, Hummer G, Szabo A, Cossio P. J Chem Phys., 2019 [10.1063/1.5118362]
Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes.
Siggel M, Bhaskara RM, Hummer G. J Phys Chem Lett., 2019 [10.1021/acs.jpclett.9b02531]
Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models.
Linker SM, Magarkar A, Köfinger J, Hummer G, Seeliger D. J Chem Theory Comput., 2019 [10.1021/acs.jctc.9b00069]
Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P(2) Synthesis.
Nishimura T, Gecht M, Covino R, Hummer G, Surma MA, Klose C, Arai H, Kono N, Stefan CJ. Mol Cell., 2019 [10.1016/j.molcel.2019.06.037]
Köfinger J, Różycki B, Hummer G. Methods Mol Biol., 2019 [10.1007/978-1-4939-9608-7_14]
Conformation space of a heterodimeric ABC exporter under turnover conditions.
Hofmann S, Januliene D, Mehdipour AR, Thomas C, Stefan E, Brüchert S, Kuhn BT, Geertsma ER, Hummer G, Tampé R, Moeller A. Nature., 2019 [10.1038/s41586-019-1391-0]
Membrane perforation by the pore-forming toxin pneumolysin.
Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G. Proc Natl Acad Sci U S A., 2019 [10.1073/pnas.1904304116]
Inward-facing conformation of a multidrug resistance MATE family transporter.
Zakrzewska S, Mehdipour AR, Malviya VN, Nonaka T, Koepke J, Muenke C, Hausner W, Hummer G, Safarian S, Michel H. Proc Natl Acad Sci U S A., 2019 [10.1073/pnas.1904210116]
Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G. Nat Commun., 2019 [10.1038/s41467-019-10345-3]
Vögele M, Köfinger J, Hummer G. J Phys Chem B., 2019 [10.1021/acs.jpcb.9b01656]
Structural basis for functional interactions in dimers of SLC26 transporters.
Chang YN, Jaumann EA, Reichel K, Hartmann J, Oliver D, Hummer G, Joseph B, Geertsma ER. Nat Commun., 2019 [10.1038/s41467-019-10001-w]
Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.
von Bülow S, Siggel M, Linke M, Hummer G. Proc Natl Acad Sci U S A., 2019 [10.1073/pnas.1817564116]
Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.
Okazaki KI, Wöhlert D, Warnau J, Jung H, Yildiz Ö, Kühlbrandt W, Hummer G. Nat Commun., 2019 [10.1038/s41467-019-09739-0]
Efficient Ensemble Refinement by Reweighting.
Köfinger J, Stelzl LS, Reuter K, Allande C, Reichel K, Hummer G. J Chem Theory Comput., 2019 [10.1021/acs.jctc.8b01231]
Perez C, Mehdipour AR, Hummer G, Locher KP. Structure., 2019 [10.1016/j.str.2019.01.013]
Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics.
Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH. Mol Cell., 2018 [10.1016/j.molcel.2018.10.035]
ATP-dependent force generation and membrane scission by ESCRT-III and Vps4.
Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH, Carlson LA, Bahrami AH, Goldman DH, Ren X, Hummer G, Bustamante C, Hurley JH. Science., 2018 [10.1126/science.aat1839]
Bock C, Löhr F, Tumulka F, Reichel K, Würz J, Hummer G, Schäfer L, Tampé R, Joseph B, Bernhard F, Dötsch V, Abele R. Sci Rep., 2018 [10.1038/s41598-018-33841-w]
Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G. J Phys Chem B., 2018 [10.1021/acs.jpcb.8b07537]
Rossini E, Gajewski J, Klaus M, Hummer G, Grininger M. Chem Commun (Camb)., 2018 [10.1039/c8cc06838k]
Biomimetic water channels: general discussion.
Baaden M, Barboiu M, Bill RM, Chen CL, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hou JL, Hummer G, Kumar M, Legrand YM, Lokesh M, Mi B, Murail S, Pohl P, Sansom M, et al. Faraday Discuss., 2018 [10.1039/c8fd90020e]
Structure and function of natural proteins for water transport: general discussion.
Baaden M, Barboiu M, Bill RM, Casanova S, Chen CL, Conner M, Freger V, Gong B, Góra A, Hinds B, Horner A, Hummer G, Kumar M, Lokesh M, Mitra S, Noy A, Pohl P, Sadet A, Sansom M, Törnroth-Horsefield S, Vashisth H. Faraday Discuss., 2018 [10.1039/c8fd90019a]
The modelling and enhancement of water hydrodynamics: general discussion.
Baaden M, Borthakur MP, Casanova S, Coalson R, Freger V, Gonzalez M, Góra A, Hinds B, Hirunpinyopas W, Hummer G, Kumar M, Lynch C, Murail S, Noy A, Sansom M, Song Q, Vashisth H, Vögele M. Faraday Discuss., 2018 [10.1039/c8fd90021c]
Applications to water transport systems: general discussion.
Baaden M, Barboiu M, Borthakur MP, Chen CL, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R, Hinds B, Hirunpinyopas W, Horner A, Hou JL, Hummer G, Iamprasertkun P, Kazushi K, Kumar M, Legrand YM, Lokesh M, Mi B, Mitra S, et al. Faraday Discuss., 2018 [10.1039/c8fd90022a]
Precision DEER Distances from Spin-Label Ensemble Refinement.
Reichel K, Stelzl LS, Köfinger J, Hummer G. J Phys Chem Lett., 2018 [10.1021/acs.jpclett.8b02439]
Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging.
Seyfried P, Heinz M, Pintér G, Klötzner DP, Becker Y, Bolte M, Jonker HRA, Stelzl LS, Hummer G, Schwalbe H, Heckel A. Chemistry., 2018 [10.1002/chem.201804040]
Redox-coupled quinone dynamics in the respiratory complex I.
Warnau J, Sharma V, Gamiz-Hernandez AP, Di Luca A, Haapanen O, Vattulainen I, Wikström M, Hummer G, Kaila VRI. Proc Natl Acad Sci U S A., 2018 [10.1073/pnas.1805468115]
Covino R, Hummer G, Ernst R. Mol Cell., 2018 [10.1016/j.molcel.2018.07.019]
Cossio P, Allegretti M, Mayer F, Müller V, Vonck J, Hummer G. Microscopy (Oxf)., 2018 [10.1093/jmicro/dfy033]
Hydrodynamics of Diffusion in Lipid Membrane Simulations.
Vögele M, Köfinger J, Hummer G. Phys Rev Lett., 2018 [10.1103/PhysRevLett.120.268104]
Molecular dynamics simulations of carbon nanotube porins in lipid bilayers.
Vögele M, Köfinger J, Hummer G. Faraday Discuss., 2018 [10.1039/c8fd00011e]
The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.
Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R. J Cell Biol., 2018 [10.1083/jcb.201802027]
De Vos O, Venable RM, Van Hecke T, Hummer G, Pastor RW, Ghysels A. J Chem Theory Comput., 2018 [10.1021/acs.jctc.8b00115]
Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.
Linke M, Köfinger J, Hummer G. J Phys Chem Lett., 2018 [10.1021/acs.jpclett.8b01090]
Transition paths in single-molecule force spectroscopy.
Cossio P, Hummer G, Szabo A. J Chem Phys., 2018 [10.1063/1.5004767]
Likelihood-based structural analysis of electron microscopy images.
Cossio P, Hummer G. Curr Opin Struct Biol., 2018 [10.1016/j.sbi.2018.03.004]
Retinal isomerization and water-pore formation in channelrhodopsin-2.
Ardevol A, Hummer G. Proc Natl Acad Sci U S A., 2018 [10.1073/pnas.1700091115]
Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.
Ramírez AS, Boilevin J, Mehdipour AR, Hummer G, Darbre T, Reymond JL, Locher KP. Nat Commun., 2018 [10.1038/s41467-018-02880-2]
Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.
Linke M, Köfinger J, Hummer G. J Phys Chem B., 2018 [10.1021/acs.jpcb.7b11988]
Cryo-EM structure of the bifunctional secretin complex of Thermus thermophilus.
D'Imprima E, Salzer R, Bhaskara RM, Sánchez R, Rose I, Kirchner L, Hummer G, Kühlbrandt W, Vonck J, Averhoff B. Elife., 2017 [10.7554/eLife.30483]
Classical Molecular Dynamics with Mobile Protons.
Lazaridis T, Hummer G. J Chem Inf Model., 2017 [10.1021/acs.jcim.7b00603]
Scaffolding the cup-shaped double membrane in autophagy.
Bahrami AH, Lin MG, Ren X, Hurley JH, Hummer G. PLoS Comput Biol., 2017 [10.1371/journal.pcbi.1005817]
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.
Stelzl LS, Kells A, Rosta E, Hummer G. J Chem Theory Comput., 2017 [10.1021/acs.jctc.7b00373]
Transition path sampling of rare events by shooting from the top.
Jung H, Okazaki KI, Hummer G. J Chem Phys., 2017 [10.1063/1.4997378]
Peptide dimerization-dissociation rates from replica exchange molecular dynamics.
Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E. J Chem Phys., 2017 [10.1063/1.5004774]
Formation and Stability of Lipid Membrane Nanotubes.
Bahrami AH, Hummer G. ACS Nano., 2017 [10.1021/acsnano.7b05542]
Stelzl LS, Erlenbach N, Heinz M, Prisner TF, Hummer G. J Am Chem Soc., 2017 [10.1021/jacs.7b05363]
Activation of the Unfolded Protein Response by Lipid Bilayer Stress.
Halbleib K, Pesek K, Covino R, Hofbauer HF, Wunnicke D, Hänelt I, Hummer G, Ernst R. Mol Cell., 2017 [10.1016/j.molcel.2017.06.012]
Kinetics from Replica Exchange Molecular Dynamics Simulations.
Stelzl LS, Hummer G. J Chem Theory Comput., 2017 [10.1021/acs.jctc.7b00372]
Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.
Chiavazzo E, Covino R, Coifman RR, Gear CW, Georgiou AS, Hummer G, Kevrekidis IG. Proc Natl Acad Sci U S A., 2017 [10.1073/pnas.1621481114]
Helical jackknives control the gates of the double-pore K(+) uptake system KtrAB.
Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I. Elife., 2017 [10.7554/eLife.24303]
Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A. Elife., 2017 [10.7554/eLife.23471]
Ghysels A, Venable RM, Pastor RW, Hummer G. J Chem Theory Comput., 2017 [10.1021/acs.jctc.7b00039]
Molecule Counts in Localization Microscopy with Organic Fluorophores.
Karathanasis C, Fricke F, Hummer G, Heilemann M. Chemphyschem., 2017 [10.1002/cphc.201601425]
Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.
Simonson T, Hummer G, Roux B. J Phys Chem A., 2017 [10.1021/acs.jpca.6b12691]
Carbon Nanotubes Mediate Fusion of Lipid Vesicles.
Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G. ACS Nano., 2017 [10.1021/acsnano.6b05434]
Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP.
Nöll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Brüchert S, Joseph B, Abele R, Oliéric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, Tampé R. Proc Natl Acad Sci U S A., 2017 [10.1073/pnas.1620009114]
Reichel K, Fisette O, Braun T, Lange OF, Hummer G, Schäfer LV. Proteins., 2016 [10.1002/prot.25224]
Model-independent counting of molecules in single-molecule localization microscopy.
Hummer G, Fricke F, Heilemann M. Mol Biol Cell., 2016 [10.1091/mbc.E16-07-0525]
Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer.
Hummer G, Szabo A. J Phys Chem B., 2016 [10.1021/acs.jpcb.6b08345]
Lehnert E, Mao J, Mehdipour AR, Hummer G, Abele R, Glaubitz C, Tampé R. J Am Chem Soc., 2016 [10.1021/jacs.6b07426]
Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy.
Cossio P, Hummer G, Szabo A. Biophys J., 2016 [10.1016/j.bpj.2016.05.054]
Cardiolipin puts the seal on ATP synthase.
Mehdipour AR, Hummer G. Proc Natl Acad Sci U S A., 2016 [10.1073/pnas.1609806113]
Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes.
Vögele M, Hummer G. J Phys Chem B., 2016 [10.1021/acs.jpcb.6b05102]
Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers.
Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. J Phys Chem Lett., 2016 [10.1021/acs.jpclett.6b00518]
A Eukaryotic Sensor for Membrane Lipid Saturation.
Covino R, Ballweg S, Stordeur C, Michaelis JB, Puth K, Wernig F, Bahrami A, Ernst AM, Hummer G, Ernst R. Mol Cell., 2016 [10.1016/j.molcel.2016.05.015]
F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements.
Sugawa M, Okazaki K, Kobayashi M, Matsui T, Hummer G, Masaike T, Nishizaka T. Proc Natl Acad Sci U S A., 2016 [10.1073/pnas.1524720113]
,font size="4">Microscopic interpretation of folding ϕ-values using the transition path ensemble.
Best RB, Hummer G. Proc Natl Acad Sci U S A., 2016 [10.1073/pnas.1520864113]
Molecular simulation and modeling of complex I.
Hummer G, Wikström M. Biochim Biophys Acta., 2016 [10.1016/j.bbabio.2016.01.005]
Bayesian ensemble refinement by replica simulations and reweighting.
Hummer G, Köfinger J. J Chem Phys., 2016 [10.1063/1.4937786]
Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch.
Blees A, Reichel K, Trowitzsch S, Fisette O, Bock C, Abele R, Hummer G, Schäfer LV, Tampé R. Sci Rep., 2015 [10.1038/srep17341]
Free energies from dynamic weighted histogram analysis using unbiased Markov state model.
Rosta E, Hummer G. J Chem Theory Comput., 2015 [10.1021/ct500719p]
On artifacts in single-molecule force spectroscopy.
Cossio P, Hummer G, Szabo A. Proc Natl Acad Sci U S A., 2015 [10.1073/pnas.1519633112]
Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Barends TR, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, et al. Science., 2015 [10.1126/science.aac5492]
Redox-induced activation of the proton pump in the respiratory complex I.
Sharma V, Belevich G, Gamiz-Hernandez AP, Róg T, Vattulainen I, Verkhovskaya ML, Wikström M, Hummer G, Kaila VR. Proc Natl Acad Sci U S A., 2015 [10.1073/pnas.1503761112]
Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase.
Okazaki K, Hummer G. Proc Natl Acad Sci U S A., 2015 [10.1073/pnas.1500691112]
Mantsyzov AB, Shen Y, Lee JH, Hummer G, Bax A. J Biomol NMR., 2015 [10.1007/s10858-015-9971-2]
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, et al. Structure., 2015 [10.1016/j.str.2015.05.013]
Johnson ME, Hummer G. Phys Rev X., 2015 [10.1103/PhysRevX.4.031037]
Kmita K, Wirth C, Warnau J, Guerrero-Castillo S, Hunte C, Hummer G, Kaila VR, Zwicker K, Brandt U, Zickermann V. Proc Natl Acad Sci U S A., 2015 [10.1073/pnas.1424353112]
Köfinger J, Ragusa MJ, Lee IH, Hummer G, Hurley JH. Structure., 2015 [10.1016/j.str.2015.02.012]
New perspectives on proton pumping in cellular respiration.
Wikström M, Sharma V, Kaila VR, Hosler JP, Hummer G. Chem Rev., 2015 [10.1021/cr500448t]
Preface: special topic on biological water.
Hummer G, Tokmakoff A. J Chem Phys., 2014 [10.1063/1.4901337]
Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VR. J Phys Chem B., 2014 [10.1021/jp508790n]
Biochemistry. Potassium ions line up.
Hummer G. Science., 2014 [10.1126/science.1260555]
Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models.
Hummer G, Szabo A. J Phys Chem B., 2014 [10.1021/jp508375q]
Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.
Nedialkova LV, Amat MA, Kevrekidis IG, Hummer G. J Chem Phys., 2014 [10.1063/1.4893963]
Mantsyzov AB, Maltsev AS, Ying J, Shen Y, Hummer G, Bax A. Protein Sci., 2014 [10.1002/pro.2511]
Kaila VR, Wikström M, Hummer G. Proc Natl Acad Sci U S A., 2014 [10.1073/pnas.1319156111]
Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.
Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA. Nat Chem., 2014 [10.1038/nchem.1898]
Calcium inhibition of ribonuclease H1 two-metal ion catalysis.
Rosta E, Yang W, Hummer G. J Am Chem Soc., 2014 [10.1021/ja411408x]
Nobel 2013 Chemistry: Methods for computational chemistry.
Thiel W, Hummer G. Nature., 2013 [10.1038/504096a]
Cossio P, Hummer G. J Struct Biol., 2013 [10.1016/j.jsb.2013.10.006]
Native contacts determine protein folding mechanisms in atomistic simulations.
Best RB, Hummer G, Eaton WA. Proc Natl Acad Sci U S A., 2013 [10.1073/pnas.1311599110]
Phosphate release coupled to rotary motion of F1-ATPase.
Okazaki K, Hummer G. Proc Natl Acad Sci U S A., 2013 [10.1073/pnas.1305497110]
Atomic-resolution structural information from scattering experiments on macromolecules in solution.
Köfinger J, Hummer G. Phys Rev E Stat Nonlin Soft Matter Phys., 2013 [10.1103/PhysRevE.87.052712]
Evolutionary pressure on the topology of protein interface interaction networks.
Johnson ME, Hummer G. J Phys Chem B., 2013 [10.1021/jp402944e]
Interface-resolved network of protein-protein interactions.
Johnson ME, Hummer G. PLoS Comput Biol., 2013 [10.1371/journal.pcbi.1003065]
The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin.
Grigoriu S, Bond R, Cossio P, Chen JA, Ly N, Hummer G, Page R, Cyert MS, Peti W. PLoS Biol., 2013 [10.1371/journal.pbio.1001492]
Theory and simulation of ion conduction in the pentameric GLIC channel.
Zhu F, Hummer G. J Chem Theory Comput., 2013 [10.1021/ct2009279]
Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À. J Am Chem Soc., 2012 [10.1021/ja310331v]
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography.
Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA. Proc Natl Acad Sci U S A., 2012 [10.1073/pnas.1210938109]
Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes.
Różycki B, Boura E, Hurley JH, Hummer G. PLoS Comput Biol., 2012 [10.1371/journal.pcbi.1002736]
Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.
Zhu F, Hummer G. Biophys J., 2012 [10.1016/j.bpj.2012.06.003]
Entropy of single-file water in (6,6) carbon nanotubes.
Waghe A, Rasaiah JC, Hummer G. J Chem Phys., 2012 [10.1063/1.4737842]
Pair diffusion, hydrodynamic interactions, and available volume in dense fluids.
Mittal J, Hummer G. J Chem Phys., 2012 [10.1063/1.4732515]
Johnson ME, Hummer G. J Phys Chem B., 2012 [10.1021/jp212611k]
Boura E, Różycki B, Chung HS, Herrick DZ, Canagarajah B, Cafiso DS, Eaton WA, Hummer G, Hurley JH. Structure., 2012 [10.1016/j.str.2012.03.008]
Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications.
Wikström M, Hummer G. Proc Natl Acad Sci U S A., 2012 [10.1073/pnas.1120949109]
Zhu F, Hummer G. J Comput Chem., 2011 [10.1002/jcc.21989]
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase.
Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W. Nat Chem Biol., 2011 [10.1038/nchembio.707]
Energetics of direct and water-mediated proton-coupled electron transfer.
Kaila VR, Hummer G. J Am Chem Soc., 2011 [10.1021/ja2082262]
Resting and active states of the ERK2:HePTP complex.
Francis DM, Różycki B, Tortajada A, Hummer G, Peti W, Page R. J Am Chem Soc., 2011 [10.1021/ja2075136]
Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.
Kim YC, Hummer G. Biochim Biophys Acta., 2011 [10.1016/j.bbabio.2011.09.004]
Diffusion models of protein folding.
Best RB, Hummer G. Phys Chem Chem Phys., 2011 [10.1039/c1cp21541h]
Single-file water in nanopores.
Köfinger J, Hummer G, Dellago C. Phys Chem Chem Phys., 2011 [10.1039/c1cp21086f]
Energetics and dynamics of proton transfer reactions along short water wires.
Kaila VR, Hummer G. Phys Chem Chem Phys., 2011 [10.1039/c1cp21112a]
Boura E, Rózycki B, Herrick DZ, Chung HS, Vecer J, Eaton WA, Cafiso DS, Hummer G, Hurley JH. Proc Natl Acad Sci U S A., 2011 [10.1073/pnas.1101763108]
Rosta E, Nowotny M, Yang W, Hummer G. J Am Chem Soc., 2011 [10.1021/ja200173a]
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions.
Różycki B, Kim YC, Hummer G. Structure., 2011 [10.1016/j.str.2010.10.006]
Crystal structure and allosteric activation of protein kinase C βII.
Leonard TA, Różycki B, Saidi LF, Hummer G, Hurley JH. Cell., 2011 [10.1016/j.cell.2010.12.013]
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks.
Johnson ME, Hummer G. Proc Natl Acad Sci U S A., 2010 [10.1073/pnas.1010954108]
Free energy profiles from single-molecule pulling experiments.
Hummer G, Szabo A. Proc Natl Acad Sci U S A., 2010 [10.1073/pnas.1015661107]
Water in the polar and nonpolar cavities of the protein interleukin-1β.
Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC. J Phys Chem B., 2010 [10.1021/jp108731r]
Interfacial thermodynamics of confined water near molecularly rough surfaces.
Mittal J, Hummer G. Faraday Discuss., 2010 [10.1039/b925913a]
Pore opening and closing of a pentameric ligand-gated ion channel.
Zhu F, Hummer G. Proc Natl Acad Sci U S A., 2010 [10.1073/pnas.1009313107]
Molecular binding: Under water's influence.
Hummer G. Nat Chem., 2010 [10.1038/nchem.885]
Biological proton pumping in an oscillating electric field.
Kim YC, Furchtgott LA, Hummer G. Phys Rev Lett., 2010 [10.1103/PhysRevLett.103.268102]
Catching a protein in the act.
Hummer G. Proc Natl Acad Sci U S A., 2010 [10.1073/pnas.0914486107]
Error and efficiency of simulated tempering simulations.
Rosta E, Hummer G. J Chem Phys., 2010 [10.1063/1.3290767]
Coordinate-dependent diffusion in protein folding.
Best RB, Hummer G. Proc Natl Acad Sci U S A., 2010 [10.1073/pnas.0910390107]
Thermostat artifacts in replica exchange molecular dynamics simulations.
Rosta E, Buchete NV, Hummer G. J Chem Theory Comput., 2010 [10.1021/ct800557h]
Error and efficiency of replica exchange molecular dynamics simulations.
Rosta E, Hummer G. J Chem Phys., 2009 [10.1063/1.3249608]
Gating transition of pentameric ligand-gated ion channels.
Zhu F, Hummer G. Biophys J., 2009 [10.1016/j.bpj.2009.08.020]
Exploration of effective potential landscapes using coarse reverse integration.
Frewen TA, Hummer G, Kevrekidis IG. J Chem Phys., 2009 [10.1063/1.3207882]
Kinetic gating of the proton pump in cytochrome c oxidase.
Kim YC, Wikström M, Hummer G. Proc Natl Acad Sci U S A., 2009 [10.1073/pnas.0903938106]
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
Best RB, Hummer G. J Phys Chem B., 2009 [10.1021/jp901540t]
Reactive flux and folding pathways in network models of coarse-grained protein dynamics.
Berezhkovskii A, Hummer G, Szabo A. J Chem Phys., 2009 [10.1063/1.3139063]
Rosta E, Woodcock HL, Brooks BR, Hummer G. J Comput Chem., 2009 [10.1002/jcc.21312]
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase.
Kaila VR, Verkhovsky MI, Hummer G, Wikström M. Biochim Biophys Acta., 2009 [10.1016/j.bbabio.2009.04.008]
A one-dimensional dipole lattice model for water in narrow nanopores.
Köfinger J, Hummer G, Dellago C. J Chem Phys., 2009 [10.1063/1.3106223]
How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study.
Turjanski AG, Hummer G, Gutkind JS. J Am Chem Soc., 2009 [10.1021/ja8071995]
Hybrid structural model of the complete human ESCRT-0 complex.
Ren X, Kloer DP, Kim YC, Ghirlando R, Saidi LF, Hummer G, Hurley JH. Structure., 2009 [10.1016/j.str.2009.01.012]
Biochemistry. Unfolding the secrets of calmodulin.
Best RB, Hummer G. Science., 2009 [10.1126/science.1169555]
Static and dynamic correlations in water at hydrophobic interfaces.
Mittal J, Hummer G. Proc Natl Acad Sci U S A., 2008 [10.1073/pnas.0809029105]
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments.
Dudko OK, Hummer G, Szabo A. Proc Natl Acad Sci U S A., 2008 [10.1073/pnas.0806085105]
Macroscopically ordered water in nanopores.
Köfinger J, Hummer G, Dellago C. Proc Natl Acad Sci U S A., 2008 [10.1073/pnas.0801448105]
Replica exchange simulations of transient encounter complexes in protein-protein association.
Kim YC, Tang C, Clore GM, Hummer G. Proc Natl Acad Sci U S A., 2008 [10.1073/pnas.0802460105]
Atomistic insights into rhodopsin activation from a dynamic model.
Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S. J Am Chem Soc., 2008 [10.1021/ja0765520]
Layering and position-dependent diffusive dynamics of confined fluids.
Mittal J, Truskett TM, Errington JR, Hummer G. Phys Rev Lett., 2008 [10.1103/PhysRevLett.100.145901]
Peptide folding kinetics from replica exchange molecular dynamics.
Buchete NV, Hummer G. Phys Rev E Stat Nonlin Soft Matter Phys., 2008 [10.1103/PhysRevE.77.030902]
Are current molecular dynamics force fields too helical?
Best RB, Buchete NV, Hummer G. Biophys J., 2008 [10.1529/biophysj.108.132696]
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase.
Kaila VR, Verkhovsky MI, Hummer G, Wikström M. Proc Natl Acad Sci U S A., 2008 [10.1073/pnas.0800770105]
Prevention of leak in the proton pump of cytochrome c oxidase.
Kaila VR, Verkhovsky M, Hummer G, Wikström M. Biochim Biophys Acta., 2008 [10.1016/j.bbabio.2008.03.016]
Binding-induced folding of a natively unstructured transcription factor.
Turjanski AG, Gutkind JS, Best RB, Hummer G. PLoS Comput Biol., 2008 [10.1371/journal.pcbi.1000060]
Dynamics of cholesterol exchange in the oxysterol binding protein family.
Canagarajah BJ, Hummer G, Prinz WA, Hurley JH. J Mol Biol., 2008 [10.1016/j.jmb.2008.01.075]
Protein folding kinetics under force from molecular simulation.
Best RB, Hummer G. J Am Chem Soc., 2008 [10.1021/ja0762691]
Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules.
Best RB, Paci E, Hummer G, Dudko OK. J Phys Chem B., 2008 [10.1021/jp075955j]
Coarse master equations for peptide folding dynamics.
Buchete NV, Hummer G. J Phys Chem B., 2008 [10.1021/jp0761665]
Water in nonpolar confinement: from nanotubes to proteins and beyond.
Rasaiah JC, Garde S, Hummer G. Annu Rev Phys Chem., 2007 [10.1146/annurev.physchem.59.032607.093815]
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
Kim YC, Hummer G. J Mol Biol., 2007 [10.1016/j.jmb.2007.11.063]
Water pulls the strings in hydrophobic polymer collapse.
Hummer G. Proc Natl Acad Sci U S A., 2007 [10.1073/pnas.0706633104]
Milac AL, Buchete NV, Fritz TA, Hummer G, Tabak LA. J Mol Biol., 2007 [10.1016/j.jmb.2007.08.028]
Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase.
Tuukkanen A, Kaila VR, Laakkonen L, Hummer G, Wikström M. Biochim Biophys Acta., 2007 [10.1016/j.bbabio.2007.06.010]
Protein conformational transitions explored by mixed elastic network models.
Zheng W, Brooks BR, Hummer G. Proteins., 2007 [10.1002/prot.21465]
The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting.
Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH. Dev Cell., 2007 [10.1016/j.devcel.2007.04.013]
Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion.
Yin H, Hummer G, Rasaiah JC. J Am Chem Soc., 2007 [10.1021/ja070456h]
Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins.
Dudko OK, Mathé J, Szabo A, Meller A, Hummer G. Biophys J., 2007 [10.1529/biophysj.106.102855]
Buchete NV, Hummer G. Biophys J., 2007 [10.1529/biophysj.106.100404]
Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.
Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM. J Mol Biol., 2007 [10.1016/j.jmb.2006.12.021]
Slow conformational dynamics and unfolding of the calmodulin C-terminal domain.
Chen YG, Hummer G. J Am Chem Soc., 2007 [10.1021/ja067791a]
Kinetic models of redox-coupled proton pumping.
Kim YC, Wikström M, Hummer G. Proc Natl Acad Sci U S A., 2007 [10.1073/pnas.0611114104]
Kinetics and mechanism of proton transport across membrane nanopores.
Dellago C, Hummer G. Phys Rev Lett., 2007 [10.1103/PhysRevLett.97.245901]
Temperature dependence of the solubility of non-polar gases in water.
Garde S, García AE, Pratt LR, Hummer G. Biophys Chem., 2006 [10.1016/s0301-4622(99)00018-6]
Berezhkovskii AM, Hummer G, Bezrukov SM. Phys Rev Lett., 2006 [10.1103/PhysRevLett.97.020601]
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.
Sriraman S, Kevrekidis IG, Hummer G. J Phys Chem B., 2006 [10.1021/jp046448u]
Diffusive model of protein folding dynamics with Kramers turnover in rate.
Best RB, Hummer G. Phys Rev Lett., 2006 [10.1103/PhysRevLett.96.228104]
Effects of electric fields on proton transport through water chains.
Hassan SA, Hummer G, Lee YS. J Chem Phys., 2006 [10.1063/1.2198820]
Intrinsic rates and activation free energies from single-molecule pulling experiments.
Dudko OK, Hummer G, Szabo A. Phys Rev Lett., 2006 [10.1103/PhysRevLett.96.108101]
Best RB, Chen YG, Hummer G. Structure., 2005 [10.1016/j.str.2005.08.009]
Effect of flexibility on hydrophobic behavior of nanotube water channels.
Andreev S, Reichman D, Hummer G. J Chem Phys., 2005 [10.1063/1.2104529]
Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM. Proc Natl Acad Sci U S A., 2005 [10.1073/pnas.0508224102]
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments.
Buchete NV, Tycko R, Hummer G. J Mol Biol., 2005 [10.1016/j.jmb.2005.08.066]
Sriraman S, Kevrekidis IG, Hummer G. Phys Rev Lett., 2005 [10.1103/PhysRevLett.95.130603]
Free energy surfaces from single-molecule force spectroscopy.
Hummer G, Szabo A. Acc Chem Res., 2005 [10.1021/ar040148d]
Peter C, Hummer G. Biophys J., 2005 [10.1529/biophysj.105.065946]
Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein".
Best RB, Hummer G. Science., 2005 [10.1126/science.1106969]
Gustchina E, Hummer G, Bewley CA, Clore GM. J Med Chem., 2005 [10.1021/jm049026h]
Reaction coordinates and rates from transition paths.
Best RB, Hummer G. Proc Natl Acad Sci U S A., 2005 [10.1073/pnas.0408098102]
Water clusters in nonpolar cavities.
Vaitheeswaran S, Yin H, Rasaiah JC, Hummer G. Proc Natl Acad Sci U S A., 2004 [10.1073/pnas.0407968101]
Hummer G, Schotte F, Anfinrud PA. Proc Natl Acad Sci U S A., 2004 [10.1073/pnas.0405295101]
Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes.
Vaitheeswaran S, Rasaiah JC, Hummer G. J Chem Phys., 2004 [10.1063/1.1796271]
Nucleic acid transport through carbon nanotube membranes.
Yeh IC, Hummer G. Proc Natl Acad Sci U S A., 2004 [10.1073/pnas.0402699101]
From transition paths to transition states and rate coefficients.
Hummer G. J Chem Phys., 2004 [10.1063/1.1630572]
Zweckstetter M, Hummer G, Bax A. Biophys J., 2004 [10.1529/biophysj.103.035790]
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.
Yeh IC, Hummer G. Biophys J., 2004 [10.1016/S0006-3495(04)74147-8]
Osmotic water transport through carbon nanotube membranes.
Kalra A, Garde S, Hummer G. Proc Natl Acad Sci U S A., 2003 [10.1073/pnas.1633354100]
Kinetics from nonequilibrium single-molecule pulling experiments.
Hummer G, Szabo A. Biophys J., 2003 [10.1016/S0006-3495(03)74449-X]
Water-gated mechanism of proton translocation by cytochrome c oxidase.
Wikström M, Verkhovsky MI, Hummer G. Biochim Biophys Acta., 2003 [10.1016/s0005-2728(03)00041-0]
Proton transport through water-filled carbon nanotubes.
Dellago C, Naor MM, Hummer G. Phys Rev Lett., 2003 [10.1103/PhysRevLett.90.105902]
Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam.
Taraphder S, Hummer G. J Am Chem Soc., 2003 [10.1021/ja016860c]
Single-file transport of water molecules through a carbon nanotube.
Berezhkovskii A, Hummer G. Phys Rev Lett., 2002 [10.1103/PhysRevLett.89.064503]
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent.
Yeh IC, Hummer G. J Am Chem Soc., 2002 [10.1021/ja025789n]
Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41.
Siebert X, Hummer G. Biochemistry., 2002 [10.1021/bi0158526]
Water conduction through the hydrophobic channel of a carbon nanotube.
Hummer G, Rasaiah JC, Noworyta JP. Nature., 2001 [10.1038/35102535]
Free energy reconstruction from nonequilibrium single-molecule pulling experiments.
Hummer G, Szabo A. Proc Natl Acad Sci U S A., 2001 [10.1073/pnas.071034098]
Ashbaugh HS, Garde S, Hummer G, Kaler EW, Paulaitis ME. Biophys J., 1999 [10.1016/S0006-3495(99)76920-1]
Conformational dynamics of cytochrome c: correlation to hydrogen exchange.
García AE, Hummer G. Proteins., 1999
Hummer G, Garde S, García AE, Paulaitis ME, Pratt LR. Proc Natl Acad Sci U S A., 1998 [10.1073/pnas.95.4.1552]
Bound water in the proton translocation mechanism of the haem-copper oxidases.
Riistama S, Hummer G, Puustinen A, Dyer RB, Woodruff WH, Wikström M. FEBS Lett., 1997 [10.1016/s0014-5793(97)01003-x]
Hydration of an alpha-helical peptide: comparison of theory and molecular dynamics simulation.
García AE, Hummer G, Soumpasis DM. Proteins., 1997
Identification of a functional water channel in cytochrome P450 enzymes.
Oprea TI, Hummer G, Garcia AE. Proc Natl Acad Sci U S A., 1997 [10.1073/pnas.94.6.2133]
Origin of Entropy Convergence in Hydrophobic Hydration and Protein Folding.
Garde S, Hummer G, García AE, Paulaitis ME, Pratt LR. Phys Rev Lett., 1996 [10.1103/PhysRevLett.77.4966]
An information theory model of hydrophobic interactions.
Hummer G, Garde S, García AE, Pohorille A, Pratt LR. Proc Natl Acad Sci U S A., 1996 [10.1073/pnas.93.17.8951]
Three-dimensional model of a selective theophylline-binding RNA molecule.
Tung CS, Oprea TI, Hummer G, García AE. J Mol Recognit., 1996 [10.1002/(SICI)1099-1352(199607)9:4%3C275::AID-JMR337%3E3.0.CO;2-8]
Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes.
Garde S, Hummer G, García AE, Pratt LR, Paulaitis ME. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics., 1996 [10.1103/physreve.53.r4310]
A statistical mechanical description of biomolecular hydration.
Hummer G, García AE, Soumpasis DM. Faraday Discuss., 1996 [10.1039/fd9960300175]
Theoretical description of biomolecular hydration. Application to A-DNA.
Garcia AE, Hummer G, Soumpasis DM. Basic Life Sci., 1996 [10.1007/978-1-4615-5847-7_26]
Hummer G, García AE, Soumpasis DM. Biophys J., 1995 [10.1016/S0006-3495(95)80381-4]
Hummer G, Soumpasis DM. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics., 1994 [10.1103/physreve.50.5085]
An extension of the rigorous base-unit oriented description of nucleic acid structures.
Tung CS, Soumpasis DM, Hummer G. J Biomol Struct Dyn., 1994 [10.1080/07391102.1994.10508071]
Hummer G, Soumpasis DM. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics., 1994 [10.1103/physreve.49.591]