Research Groups

 

Publications of Gerhard Hummer (Results: 285)

 

Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase.
Proceedings of the National Academy of Sciences of the United States of America
Blanc FEC, Hummer G PubMed
Mar 2024 Volume: 121 Issue: 11 Pages: e2314199121

Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.
Cell
Tsai YX, Chang NE, Reuter K, Chang HT, Yang TJ, von Bülow S, Sehrawat V, Zerrouki N, Tuffery M, Gecht M, Grothaus IL, Colombi Ciacchi L, Wang YS, Hsu MF, Khoo KH, Hummer G, Hsu SD, Hanus C, Sikora M PubMed
Feb 2024 Volume: 187 Issue: 5 Pages: 1296-1311.e26

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca-sensor ALG-2.
Proceedings of the National Academy of Sciences of the United States of America
Shukla S, Chen W, Rao S, Yang S, Ou C, Larsen KP, Hummer G, Hanson PI, Hurley JH PubMed
Feb 2024 Volume: 121 Issue: 9 Pages: e2318046121

Hierarchical Assembly of Single-Stranded RNA.
Journal of chemical theory and computation
Pietrek LM, Stelzl LS, Hummer G PubMed
Mar 2024 Volume: 20 Issue: 5 Pages: 2246-2260

Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore.
Science advances
Rao S, Skulsuppaisarn M, Strong LM, Ren X, Lazarou M, Hurley JH, Hummer G PubMed
Feb 2024 Volume: 10 Issue: 6 Pages: eadj8027

Tracing the substrate translocation mechanism in P-glycoprotein.
eLife
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q PubMed
Jan 2024 Volume: 12 Issue: Pages:

Machine-guided path sampling to discover mechanisms of molecular self-organization.
Nature computational science
Jung H, Covino R, Arjun A, Leitold C, Dellago C, Bolhuis PG, Hummer G PubMed
Apr 2023 Volume: 3 Issue: 4 Pages: 334-345

Neighbor List Artifacts in Molecular Dynamics Simulations.
Journal of chemical theory and computation
Kim H, Fábián B, Hummer G PubMed
Dec 2023 Volume: 19 Issue: 23 Pages: 8919-8929

Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides.
Nature communications
Pandi A, Adam D, Zare A, Trinh VT, Schaefer SL, Burt M, Klabunde B, Bobkova E, Kushwaha M, Foroughijabbari Y, Braun P, Spahn C, Preußer C, Pogge von Strandmann E, Bode HB, von Buttlar H, Bertrams W, Jung AL, Abendroth F, Schmeck B, Hummer G, Vázquez O, Erb TJ PubMed
Nov 2023 Volume: 14 Issue: 1 Pages: 7197

Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca-sensor ALG-2.
bioRxiv : the preprint server for biology
Shukla S, Chen W, Rao S, Yang S, Ou C, Larsen KP, Hummer G, Hanson PI, Hurley JH PubMed
Oct 2023 Volume: Issue: Pages:

Efficient generation of random rotation matrices in four dimensions.
Physical review. E
Bullerjahn JT, Fábián B, Hummer G PubMed
Sep 2023 Volume: 108 Issue: 3-2 Pages: 035307

Martini 3 Coarse-Grained Force Field for Cholesterol.
Journal of chemical theory and computation
Borges-Araújo L, Borges-Araújo AC, Ozturk TN, Ramirez-Echemendia DP, Fábián B, Carpenter TS, Thallmair S, Barnoud J, Ingólfsson HI, Hummer G, Tieleman DP, Marrink SJ, Souza PCT, Melo MN PubMed
Oct 2023 Volume: 19 Issue: 20 Pages: 7387-7404

Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments.
Nature structural & molecular biology
Oosterheert W, Blanc FEC, Roy A, Belyy A, Sanders MB, Hofnagel O, Hummer G, Bieling P, Raunser S PubMed
Nov 2023 Volume: 30 Issue: 11 Pages: 1774-1785

Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel.
Current biology : CB
Hanson SM, Scholüke J, Liewald J, Sharma R, Ruse C, Engel M, Schüler C, Klaus A, Arghittu S, Baumbach F, Seidenthal M, Dill H, Hummer G, Gottschalk A PubMed
Aug 2023 Volume: 33 Issue: 16 Pages: 3423-3435.e5

Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity.
Nature communications
Goretzki B, Wiedemann C, McCray BA, Schäfer SL, Jansen J, Tebbe F, Mitrovic SA, Nöth J, Cabezudo AC, Donohue JK, Jeffries CM, Steinchen W, Stengel F, Sumner CJ, Hummer G, Hellmich UA PubMed
Jul 2023 Volume: 14 Issue: 1 Pages: 4165

Unwrapping NPT Simulations to Calculate Diffusion Coefficients.
Journal of chemical theory and computation
Bullerjahn JT, von Bülow S, Heidari M, Hénin J, Hummer G PubMed
Jun 2023 Volume: 19 Issue: 11 Pages: 3406-3417

Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum.
Nature
González A, Covarrubias-Pinto A, Bhaskara RM, Glogger M, Kuncha SK, Xavier A, Seemann E, Misra M, Hoffmann ME, Bräuning B, Balakrishnan A, Qualmann B, Dötsch V, Schulman BA, Kessels MM, Hübner CA, Heilemann M, Hummer G, Dikić I PubMed
Jun 2023 Volume: 618 Issue: 7964 Pages: 394-401

Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy.
Nature
Foronda H, Fu Y, Covarrubias-Pinto A, Bocker HT, González A, Seemann E, Franzka P, Bock A, Bhaskara RM, Liebmann L, Hoffmann ME, Katona I, Koch N, Weis J, Kurth I, Gleeson JG, Reggiori F, Hummer G, Kessels MM, Qualmann B, Mari M, Dikić I, Hübner CA PubMed
Jun 2023 Volume: 618 Issue: 7964 Pages: 402-410

Structure and assembly of a bacterial gasdermin pore.
bioRxiv : the preprint server for biology
Johnson AG, Mayer ML, Schaefer SL, McNamara-Bordewick NK, Hummer G, Kranzusch PJ PubMed
Oct 2023 Volume: Issue: Pages:

Visualizing the disordered nuclear transport machinery in situ.
Nature
Yu M, Heidari M, Mikhaleva S, Tan PS, Mingu S, Ruan H, Reinkemeier CD, Obarska-Kosinska A, Siggel M, Beck M, Hummer G, Lemke EA PubMed
May 2023 Volume: 617 Issue: 7959 Pages: 162-169

Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors.
Cell chemical biology
Lettl C, Schindele F, Mehdipour AR, Steiner T, Ring D, Brack-Werner R, Stecher B, Eisenreich W, Bilitewski U, Hummer G, Witschel M, Fischer W, Haas R PubMed
May 2023 Volume: 30 Issue: 5 Pages: 499-512.e5

Dissecting the conformational complexity and mechanism of a bacterial heme transporter.
Nature chemical biology
Wu D, Mehdipour AR, Finke F, Goojani HG, Groh RR, Grund TN, Reichhart TMB, Zimmermann R, Welsch S, Bald D, Shepherd M, Hummer G, Safarian S PubMed
Aug 2023 Volume: 19 Issue: 8 Pages: 992-1003

Author Correction: Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level.
Nature communications
Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P PubMed
Feb 2023 Volume: 14 Issue: 1 Pages: 1142

Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol.
Journal of chemical theory and computation
Fábián B, Thallmair S, Hummer G PubMed
Mar 2023 Volume: 19 Issue: 5 Pages: 1592-1601

Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants.
PLoS computational biology
von Bülow S, Sikora M, Blanc FEC, Covino R, Hummer G PubMed
Jan 2023 Volume: 19 Issue: 1 Pages: e1010822

Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level.
Nature communications
Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P PubMed
Dec 2022 Volume: 13 Issue: 1 Pages: 7926

Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery.
Science advances
Jensen LE, Rao S, Schuschnig M, Cada AK, Martens S, Hummer G, Hurley JH PubMed
Dec 2022 Volume: 8 Issue: 50 Pages: eadd1436

Structural ensembles of disordered proteins from hierarchical chain growth and simulation.
Current opinion in structural biology
Pietrek LM, Stelzl LS, Hummer G PubMed
Feb 2023 Volume: 78 Issue: Pages: 102501

Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions.
The Journal of chemical physics
Linke M, Quoika PK, Bramas B, Köfinger J, Hummer G PubMed
Nov 2022 Volume: 157 Issue: 20 Pages: 204802

Sublytic gasdermin-D pores captured in atomistic molecular simulations.
eLife
Schaefer SL, Hummer G PubMed
Nov 2022 Volume: 11 Issue: Pages:

TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes.
The Journal of chemical physics
Siggel M, Kehl S, Reuter K, Köfinger J, Hummer G PubMed
Nov 2022 Volume: 157 Issue: 17 Pages: 174801

In situ structural analysis reveals membrane shape transitions during autophagosome formation.
Proceedings of the National Academy of Sciences of the United States of America
Bieber A, Capitanio C, Erdmann PS, Fiedler F, Beck F, Lee CW, Li D, Hummer G, Schulman BA, Baumeister W, Wilfling F PubMed
Sep 2022 Volume: 119 Issue: 39 Pages: e2209823119

Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly.
ACS applied bio materials
Vögele M, Köfinger J, Hummer G PubMed
Feb 2024 Volume: 7 Issue: 2 Pages: 528-534

Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC.
Cell
Sušac L, Vuong MT, Thomas C, von Bülow S, O'Brien-Ball C, Santos AM, Fernandes RA, Hummer G, Tampé R, Davis SJ PubMed
Aug 2022 Volume: 185 Issue: 17 Pages: 3201-3213.e19

Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations.
The journal of physical chemistry letters
Palacio-Rodriguez K, Vroylandt H, Stelzl LS, Pietrucci F, Hummer G, Cossio P PubMed
Aug 2022 Volume: 13 Issue: 32 Pages: 7490-7496

Small ionic radii limit time step in Martini 3 molecular dynamics simulations.
The Journal of chemical physics
Fábián B, Thallmair S, Hummer G PubMed
Jul 2022 Volume: 157 Issue: 3 Pages: 034101

Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism.
The EMBO journal
Khera R, Mehdipour AR, Bolla JR, Kahnt J, Welsch S, Ermler U, Muenke C, Robinson CV, Hummer G, Xie H, Michel H PubMed
Sep 2022 Volume: 41 Issue: 18 Pages: e109990

AI-based structure prediction empowers integrative structural analysis of human nuclear pores.
Science (New York, N.Y.)
Mosalaganti S, Obarska-Kosinska A, Siggel M, Taniguchi R, Turoňová B, Zimmerli CE, Buczak K, Schmidt FH, Margiotta E, Mackmull MT, Hagen WJH, Hummer G, Kosinski J, Beck M PubMed
Jun 2022 Volume: 376 Issue: 6598 Pages: eabm9506

Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure.
JACS Au
Stelzl LS, Pietrek LM, Holla A, Oroz J, Sikora M, Köfinger J, Schuler B, Zweckstetter M, Hummer G PubMed
Mar 2022 Volume: 2 Issue: 3 Pages: 673-686

Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes.
Molecular cell
Cullati SN, Chaikuad A, Chen JS, Gebel J, Tesmer L, Zhubi R, Navarrete-Perea J, Guillen RX, Gygi SP, Hummer G, Dötsch V, Knapp S, Gould KL PubMed
Jun 2022 Volume: 82 Issue: 11 Pages: 2006-2020.e8

Co-translational assembly orchestrates competing biogenesis pathways.
Nature communications
Seidel M, Becker A, Pereira F, Landry JJM, de Azevedo NTD, Fusco CM, Kaindl E, Romanov N, Baumbach J, Langer JD, Schuman EM, Patil KR, Hummer G, Benes V, Beck M PubMed
Mar 2022 Volume: 13 Issue: 1 Pages: 1224

Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter.
Nature communications
Lambert E, Mehdipour AR, Schmidt A, Hummer G, Perez C PubMed
Feb 2022 Volume: 13 Issue: 1 Pages: 1022

Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation.
The EMBO journal
Gruijs da Silva LA, Simonetti F, Hutten S, Riemenschneider H, Sternburg EL, Pietrek LM, Gebel J, Dötsch V, Edbauer D, Hummer G, Stelzl LS, Dormann D PubMed
Apr 2022 Volume: 41 Issue: 8 Pages: e108443

Solution Structure and Conformational Flexibility of a Polyketide Synthase Module.
JACS Au
Klaus M, Rossini E, Linden A, Paithankar KS, Zeug M, Ignatova Z, Urlaub H, Khosla C, Köfinger J, Hummer G, Grininger M PubMed
Dec 2021 Volume: 1 Issue: 12 Pages: 2162-2171

Nuclear pores dilate and constrict in cellulo.
Science (New York, N.Y.)
Zimmerli CE, Allegretti M, Rantos V, Goetz SK, Obarska-Kosinska A, Zagoriy I, Halavatyi A, Hummer G, Mahamid J, Kosinski J, Beck M PubMed
Dec 2021 Volume: 374 Issue: 6573 Pages: eabd9776

The structure of the MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily.
Proceedings of the National Academy of Sciences of the United States of America
Zhao J, Xie H, Mehdipour AR, Safarian S, Ermler U, Münke C, Thielmann Y, Hummer G, Ebersberger I, Wang J, Michel H PubMed
Nov 2021 Volume: 118 Issue: 46 Pages:

Structural basis of polyamine transport by human ATP13A2 (PARK9).
Molecular cell
Sim SI, von Bülow S, Hummer G, Park E PubMed
Nov 2021 Volume: 81 Issue: 22 Pages: 4635-4649.e8

The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB.
Nature communications
Safarian S, Opel-Reading HK, Wu D, Mehdipour AR, Hards K, Harold LK, Radloff M, Stewart I, Welsch S, Hummer G, Cook GM, Krause KL, Michel H PubMed
Sep 2021 Volume: 12 Issue: 1 Pages: 5236

Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control.
EMBO reports
Reggio A, Buonomo V, Berkane R, Bhaskara RM, Tellechea M, Peluso I, Polishchuk E, Di Lorenzo G, Cirillo C, Esposito M, Hussain A, Huebner AK, Hübner CA, Settembre C, Hummer G, Grumati P, Stolz A PubMed
Sep 2021 Volume: 22 Issue: 9 Pages: e52289

Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane.
The journal of physical chemistry. B
Schaefer SL, Jung H, Hummer G PubMed
Jul 2021 Volume: 125 Issue: 28 Pages: 7732-7741

Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments.
The Journal of chemical physics
Bullerjahn JT, Hummer G PubMed
Jun 2021 Volume: 154 Issue: 23 Pages: 234105

Famotidine inhibits toll-like receptor 3-mediated inflammatory signaling in SARS-CoV-2 infection.
The Journal of biological chemistry
Mukherjee R, Bhattacharya A, Bojkova D, Mehdipour AR, Shin D, Khan KS, Hei-Yin Cheung H, Wong KB, Ng WL, Cinatl J, Geurink PP, van der Heden van Noort GJ, Rajalingam K, Ciesek S, Hummer G, Dikic I PubMed
Aug 2021 Volume: 297 Issue: 2 Pages: 100925

Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1.
The Journal of cell biology
Väth K, Mattes C, Reinhard J, Covino R, Stumpf H, Hummer G, Ernst R PubMed
Aug 2021 Volume: 220 Issue: 8 Pages:

Membrane fusion and drug delivery with carbon nanotube porins.
Proceedings of the National Academy of Sciences of the United States of America
Ho NT, Siggel M, Camacho KV, Bhaskara RM, Hicks JM, Yao YC, Zhang Y, Köfinger J, Hummer G, Noy A PubMed
May 2021 Volume: 118 Issue: 19 Pages:

Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike.
Proceedings of the National Academy of Sciences of the United States of America
Mehdipour AR, Hummer G PubMed
May 2021 Volume: 118 Issue: 19 Pages:

Computational epitope map of SARS-CoV-2 spike protein.
PLoS computational biology
Sikora M, von Bülow S, Blanc FEC, Gecht M, Covino R, Hummer G PubMed
Apr 2021 Volume: 17 Issue: 4 Pages: e1008790

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition).
Autophagy
Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, Abeliovich H, Abildgaard MH, Abudu YP, Acevedo-Arozena A, Adamopoulos IE, Adeli K, Adolph TE, Adornetto A, Aflaki E, Agam G, Agarwal A, Aggarwal BB, Agnello M, Agostinis P, Agrewala JN, Agrotis A, Aguilar PV, Ahmad ST, Ahmed ZM, Ahumada-Castro U, Aits S, Aizawa S, Akkoc Y, Akoumianaki T, Akpinar HA, Al-Abd AM, Al-Akra L, Al-Gharaibeh A, Alaoui-Jamali MA, Alberti S, Alcocer-Gómez E, Alessandri C, Ali M, Alim Al-Bari MA, Al... PubMed
Jan 2021 Volume: 17 Issue: 1 Pages: 1-382

FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes.
The journal of physical chemistry letters
Siggel M, Bhaskara RM, Moesser MK, D Ikić I, Hummer G PubMed
Feb 2021 Volume: 12 Issue: 7 Pages: 1926-1931

Structural biology in the fight against COVID-19.
Nature structural & molecular biology
Bárcena M, Barnes CO, Beck M, Bjorkman PJ, Canard B, Gao GF, Gao Y, Hilgenfeld R, Hummer G, Patwardhan A, Santoni G, Saphire EO, Schaffitzel C, Schendel SL, Smith JL, Thorn A, Veesler D, Zhang P, Zhou Q PubMed
Jan 2021 Volume: 28 Issue: 1 Pages: 2-7

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model.
Journal of chemical theory and computation
Benayad Z, von Bülow S, Stelzl LS, Hummer G PubMed
Jan 2021 Volume: 17 Issue: 1 Pages: 525-537

Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection.
eLife
Shin D, Bhattacharya A, Cheng YL, Alonso MC, Mehdipour AR, van der Heden van Noort GJ, Ovaa H, Hummer G, Dikic I PubMed
Nov 2020 Volume: 9 Issue: Pages:

Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems.
Chemical reviews
Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D PubMed
Oct 2021 Volume: 121 Issue: 19 Pages: 11701-11725

MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations.
The Journal of chemical physics
Gecht M, Siggel M, Linke M, Hummer G, Köfinger J PubMed
Oct 2020 Volume: 153 Issue: 14 Pages: 144105

Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography.
Proceedings of the National Academy of Sciences of the United States of America
Sikora M, Ermel UH, Seybold A, Kunz M, Calloni G, Reitz J, Vabulas RM, Hummer G, Frangakis AS PubMed
Nov 2020 Volume: 117 Issue: 44 Pages: 27132-27140

Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation.
Science (New York, N.Y.)
Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S PubMed
Sep 2020 Volume: 369 Issue: 6508 Pages:

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges.
Science (New York, N.Y.)
Turoňová B, Sikora M, Schürmann C, Hagen WJH, Welsch S, Blanc FEC, von Bülow S, Gecht M, Bagola K, Hörner C, van Zandbergen G, Landry J, de Azevedo NTD, Mosalaganti S, Schwarz A, Covino R, Mühlebach MD, Hummer G, Krijnse Locker J, Beck M PubMed
Oct 2020 Volume: 370 Issue: 6513 Pages: 203-208

Compaction of RNA Duplexes in the Cell*.
Angewandte Chemie (International ed. in English)
Collauto A, von Bülow S, Gophane DB, Saha S, Stelzl LS, Hummer G, Sigurdsson ST, Prisner TF PubMed
Dec 2020 Volume: 59 Issue: 51 Pages: 23025-23029

Validation tests for cryo-EM maps using an independent particle set.
Journal of structural biology: X
Ortiz S, Stanisic L, Rodriguez BA, Rampp M, Hummer G, Cossio P PubMed
2020 Volume: 4 Issue: Pages: 100032

Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity.
Nature
Shin D, Mukherjee R, Grewe D, Bojkova D, Baek K, Bhattacharya A, Schulz L, Widera M, Mehdipour AR, Tascher G, Geurink PP, Wilhelm A, van der Heden van Noort GJ, Ovaa H, Müller S, Knobeloch KP, Rajalingam K, Schulman BA, Cinatl J, Hummer G, Ciesek S, Dikic I PubMed
Nov 2020 Volume: 587 Issue: 7835 Pages: 657-662

p63 uses a switch-like mechanism to set the threshold for induction of apoptosis.
Nature chemical biology
Gebel J, Tuppi M, Chaikuad A, Hötte K, Schröder M, Schulz L, Löhr F, Gutfreund N, Finke F, Henrich E, Mezhyrova J, Lehnert R, Pampaloni F, Hummer G, Stelzer EHK, Knapp S, Dötsch V PubMed
Oct 2020 Volume: 16 Issue: 10 Pages: 1078-1086

Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure.
The Journal of chemical physics
von Bülow S, Bullerjahn JT, Hummer G PubMed
Jul 2020 Volume: 153 Issue: 2 Pages: 021101

Optimal estimates of self-diffusion coefficients from molecular dynamics simulations.
The Journal of chemical physics
Bullerjahn JT, von Bülow S, Hummer G PubMed
Jul 2020 Volume: 153 Issue: 2 Pages: 024116

Quantifying Protein-Protein Interactions in Molecular Simulations.
The journal of physical chemistry. B
Jost Lopez A, Quoika PK, Linke M, Hummer G, Köfinger J PubMed
Jun 2020 Volume: 124 Issue: 23 Pages: 4673-4685

Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex.
Science (New York, N.Y.)
Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA PubMed
Apr 2020 Volume: 368 Issue: 6489 Pages:

Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation.
Proceedings of the National Academy of Sciences of the United States of America
Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G PubMed
Mar 2020 Volume: 117 Issue: 10 Pages: 5109-5110

Regulation of lipid saturation without sensing membrane fluidity.
Nature communications
Ballweg S, Sezgin E, Doktorova M, Covino R, Reinhard J, Wunnicke D, Hänelt I, Levental I, Hummer G, Ernst R PubMed
Feb 2020 Volume: 11 Issue: 1 Pages: 756

Ion Binding and Selectivity of the Na/H Antiporter MjNhaP1 from Experiment and Simulation.
The journal of physical chemistry. B
Warnau J, Wöhlert D, Okazaki KI, Yildiz Ö, Gamiz-Hernandez AP, Kaila VRI, Kühlbrandt W, Hummer G PubMed
Jan 2020 Volume: 124 Issue: 2 Pages: 336-344

Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations.
Journal of chemical theory and computation
Pietrek LM, Stelzl LS, Hummer G PubMed
Jan 2020 Volume: 16 Issue: 1 Pages: 725-737

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.
Structure (London, England : 1993)
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, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A PubMed
Dec 2019 Volume: 27 Issue: 12 Pages: 1745-1759

High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label.
Nucleic acids research
Heinz M, Erlenbach N, Stelzl LS, Thierolf G, Kamble NR, Sigurdsson ST, Prisner TF, Hummer G PubMed
Jan 2020 Volume: 48 Issue: 2 Pages: 924-933

Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.
Molecular cell
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 PubMed
Jan 2020 Volume: 77 Issue: 1 Pages: 164-179.e6

TBK1-mediated phosphorylation of LC3C and GABARAP-L2 controls autophagosome shedding by ATG4 protease.
EMBO reports
Herhaus L, Bhaskara RM, Lystad AH, Gestal-Mato U, Covarrubias-Pinto A, Bonn F, Simonsen A, Hummer G, Dikic I PubMed
Jan 2020 Volume: 21 Issue: 1 Pages: e48317

Molecular free energy profiles from force spectroscopy experiments by inversion of observed committors.
The Journal of chemical physics
Covino R, Woodside MT, Hummer G, Szabo A, Cossio P PubMed
Oct 2019 Volume: 151 Issue: 15 Pages: 154115

Phospholipid Scramblases Remodel the Shape of Asymmetric Membranes.
The journal of physical chemistry letters
Siggel M, Bhaskara RM, Hummer G PubMed
Oct 2019 Volume: 10 Issue: 20 Pages: 6351-6354

Fragment Binding Pose Predictions Using Unbiased Simulations and Markov-State Models.
Journal of chemical theory and computation
Linker SM, Magarkar A, Köfinger J, Hummer G, Seeliger D PubMed
Sep 2019 Volume: 15 Issue: 9 Pages: 4974-4981

Osh Proteins Control Nanoscale Lipid Organization Necessary for PI(4,5)P Synthesis.
Molecular cell
Nishimura T, Gecht M, Covino R, Hummer G, Surma MA, Klose C, Arai H, Kono N, Stefan CJ PubMed
Sep 2019 Volume: 75 Issue: 5 Pages: 1043-1057.e8

Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods.
Methods in molecular biology (Clifton, N.J.)
Köfinger J, Różycki B, Hummer G PubMed
2019 Volume: 2022 Issue: Pages: 341-352

Conformation space of a heterodimeric ABC exporter under turnover conditions.
Nature
Hofmann S, Januliene D, Mehdipour AR, Thomas C, Stefan E, Brüchert S, Kuhn BT, Geertsma ER, Hummer G, Tampé R, Moeller A PubMed
Jul 2019 Volume: 571 Issue: 7766 Pages: 580-583

Membrane perforation by the pore-forming toxin pneumolysin.
Proceedings of the National Academy of Sciences of the United States of America
Vögele M, Bhaskara RM, Mulvihill E, van Pee K, Yildiz Ö, Kühlbrandt W, Müller DJ, Hummer G PubMed
Jul 2019 Volume: 116 Issue: 27 Pages: 13352-13357

Inward-facing conformation of a multidrug resistance MATE family transporter.
Proceedings of the National Academy of Sciences of the United States of America
Zakrzewska S, Mehdipour AR, Malviya VN, Nonaka T, Koepke J, Muenke C, Hausner W, Hummer G, Safarian S, Michel H PubMed
Jun 2019 Volume: 116 Issue: 25 Pages: 12275-12284

Curvature induction and membrane remodeling by FAM134B reticulon homology domain assist selective ER-phagy.
Nature communications
Bhaskara RM, Grumati P, Garcia-Pardo J, Kalayil S, Covarrubias-Pinto A, Chen W, Kudryashev M, Dikic I, Hummer G PubMed
May 2019 Volume: 10 Issue: 1 Pages: 2370

Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations.
The journal of physical chemistry. B
Vögele M, Köfinger J, Hummer G PubMed
Jun 2019 Volume: 123 Issue: 24 Pages: 5099-5106

Structural basis for functional interactions in dimers of SLC26 transporters.
Nature communications
Chang YN, Jaumann EA, Reichel K, Hartmann J, Oliver D, Hummer G, Joseph B, Geertsma ER PubMed
May 2019 Volume: 10 Issue: 1 Pages: 2032

Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.
Proceedings of the National Academy of Sciences of the United States of America
von Bülow S, Siggel M, Linke M, Hummer G PubMed
May 2019 Volume: 116 Issue: 20 Pages: 9843-9852

Mechanism of the electroneutral sodium/proton antiporter PaNhaP from transition-path shooting.
Nature communications
Okazaki KI, Wöhlert D, Warnau J, Jung H, Yildiz Ö, Kühlbrandt W, Hummer G PubMed
Apr 2019 Volume: 10 Issue: 1 Pages: 1742

Efficient Ensemble Refinement by Reweighting.
Journal of chemical theory and computation
Köfinger J, Stelzl LS, Reuter K, Allande C, Reichel K, Hummer G PubMed
May 2019 Volume: 15 Issue: 5 Pages: 3390-3401

Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation.
Structure (London, England : 1993)
Perez C, Mehdipour AR, Hummer G, Locher KP PubMed
Apr 2019 Volume: 27 Issue: 4 Pages: 669-678.e5

Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics.
Molecular cell
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 PubMed
Jan 2019 Volume: 73 Issue: 2 Pages: 339-353.e6

ATP-dependent force generation and membrane scission by ESCRT-III and Vps4.
Science (New York, N.Y.)
Schöneberg J, Pavlin MR, Yan S, Righini M, Lee IH, Carlson LA, Bahrami AH, Goldman DH, Ren X, Hummer G, Bustamante C, Hurley JH PubMed
Dec 2018 Volume: 362 Issue: 6421 Pages: 1423-1428

Structural and functional insights into the interaction and targeting hub TMD0 of the polypeptide transporter TAPL.
Scientific reports
Bock C, Löhr F, Tumulka F, Reichel K, Würz J, Hummer G, Schäfer L, Tampé R, Joseph B, Bernhard F, Dötsch V, Abele R PubMed
Oct 2018 Volume: 8 Issue: 1 Pages: 15662

Dispersion Correction Alleviates Dye Stacking of Single-Stranded DNA and RNA in Simulations of Single-Molecule Fluorescence Experiments.
The journal of physical chemistry. B
Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G PubMed
Dec 2018 Volume: 122 Issue: 49 Pages: 11626-11639

Analysis and engineering of substrate shuttling by the acyl carrier protein (ACP) in fatty acid synthases (FASs).
Chemical communications (Cambridge, England)
Rossini E, Gajewski J, Klaus M, Hummer G, Grininger M PubMed
Oct 2018 Volume: 54 Issue: 82 Pages: 11606-11609

Biomimetic water channels: general discussion.
Faraday discussions
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, Song Q, Song W, Törnroth-Horsefield S, Vashisth H, Vögele M PubMed
Sep 2018 Volume: 209 Issue: 0 Pages: 205-229

Structure and function of natural proteins for water transport: general discussion.
Faraday discussions
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 PubMed
Sep 2018 Volume: 209 Issue: 0 Pages: 83-95

The modelling and enhancement of water hydrodynamics: general discussion.
Faraday discussions
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 PubMed
Sep 2018 Volume: 209 Issue: 0 Pages: 273-285

Applications to water transport systems: general discussion.
Faraday discussions
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, Murail S, Noy A, Nunes S, Pohl P, Song Q, Song W, Tornroth-Horsefield S, Vashisth H PubMed
Sep 2018 Volume: 209 Issue: 0 Pages: 389-414

Precision DEER Distances from Spin-Label Ensemble Refinement.
The journal of physical chemistry letters
Reichel K, Stelzl LS, Köfinger J, Hummer G PubMed
Oct 2018 Volume: 9 Issue: 19 Pages: 5748-5752

Optimal Destabilization of DNA Double Strands by Single-Nucleobase Caging.
Chemistry (Weinheim an der Bergstrasse, Germany)
Seyfried P, Heinz M, Pintér G, Klötzner DP, Becker Y, Bolte M, Jonker HRA, Stelzl LS, Hummer G, Schwalbe H, Heckel A PubMed
Nov 2018 Volume: 24 Issue: 66 Pages: 17568-17576

Redox-coupled quinone dynamics in the respiratory complex I.
Proceedings of the National Academy of Sciences of the United States of America
Warnau J, Sharma V, Gamiz-Hernandez AP, Di Luca A, Haapanen O, Vattulainen I, Wikström M, Hummer G, Kaila VRI PubMed
Sep 2018 Volume: 115 Issue: 36 Pages: E8413-E8420

Integrated Functions of Membrane Property Sensors and a Hidden Side of the Unfolded Protein Response.
Molecular cell
Covino R, Hummer G, Ernst R PubMed
Aug 2018 Volume: 71 Issue: 3 Pages: 458-467

Bayesian inference of rotor ring stoichiometry from electron microscopy images of archaeal ATP synthase.
Microscopy (Oxford, England)
Cossio P, Allegretti M, Mayer F, Müller V, Vonck J, Hummer G PubMed
Oct 2018 Volume: 67 Issue: 5 Pages: 266-273

Hydrodynamics of Diffusion in Lipid Membrane Simulations.
Physical review letters
Vögele M, Köfinger J, Hummer G PubMed
Jun 2018 Volume: 120 Issue: 26 Pages: 268104

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers.
Faraday discussions
Vögele M, Köfinger J, Hummer G PubMed
Sep 2018 Volume: 209 Issue: 0 Pages: 341-358

The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.
The Journal of cell biology
Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R PubMed
Sep 2018 Volume: 217 Issue: 9 Pages: 3109-3126

Membrane Permeability: Characteristic Times and Lengths for Oxygen and a Simulation-Based Test of the Inhomogeneous Solubility-Diffusion Model.
Journal of chemical theory and computation
De Vos O, Venable RM, Van Hecke T, Hummer G, Pastor RW, Ghysels A PubMed
Jul 2018 Volume: 14 Issue: 7 Pages: 3811-3824

Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations.
The journal of physical chemistry letters
Linke M, Köfinger J, Hummer G PubMed
Jun 2018 Volume: 9 Issue: 11 Pages: 2874-2878

Transition paths in single-molecule force spectroscopy.
The Journal of chemical physics
Cossio P, Hummer G, Szabo A PubMed
Mar 2018 Volume: 148 Issue: 12 Pages: 123309

Likelihood-based structural analysis of electron microscopy images.
Current opinion in structural biology
Cossio P, Hummer G PubMed
Apr 2018 Volume: 49 Issue: Pages: 162-168

Retinal isomerization and water-pore formation in channelrhodopsin-2.
Proceedings of the National Academy of Sciences of the United States of America
Ardevol A, Hummer G PubMed
Apr 2018 Volume: 115 Issue: 14 Pages: 3557-3562

Structural basis of the molecular ruler mechanism of a bacterial glycosyltransferase.
Nature communications
Ramírez AS, Boilevin J, Mehdipour AR, Hummer G, Darbre T, Reymond JL, Locher KP PubMed
Jan 2018 Volume: 9 Issue: 1 Pages: 445

Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations.
The journal of physical chemistry. B
Linke M, Köfinger J, Hummer G PubMed
May 2018 Volume: 122 Issue: 21 Pages: 5630-5639

Cryo-EM structure of the bifunctional secretin complex of .
eLife
D'Imprima E, Salzer R, Bhaskara RM, Sánchez R, Rose I, Kirchner L, Hummer G, Kühlbrandt W, Vonck J, Averhoff B PubMed
Dec 2017 Volume: 6 Issue: Pages:

Classical Molecular Dynamics with Mobile Protons.
Journal of chemical information and modeling
Lazaridis T, Hummer G PubMed
Nov 2017 Volume: 57 Issue: 11 Pages: 2833-2845

Scaffolding the cup-shaped double membrane in autophagy.
PLoS computational biology
Bahrami AH, Lin MG, Ren X, Hurley JH, Hummer G PubMed
Oct 2017 Volume: 13 Issue: 10 Pages: e1005817

Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations.
Journal of chemical theory and computation
Stelzl LS, Kells A, Rosta E, Hummer G PubMed
Dec 2017 Volume: 13 Issue: 12 Pages: 6328-6342

Transition path sampling of rare events by shooting from the top.
The Journal of chemical physics
Jung H, Okazaki KI, Hummer G PubMed
Oct 2017 Volume: 147 Issue: 15 Pages: 152716

Peptide dimerization-dissociation rates from replica exchange molecular dynamics.
The Journal of chemical physics
Leahy CT, Kells A, Hummer G, Buchete NV, Rosta E PubMed
Oct 2017 Volume: 147 Issue: 15 Pages: 152725

Formation and Stability of Lipid Membrane Nanotubes.
ACS nano
Bahrami AH, Hummer G PubMed
Sep 2017 Volume: 11 Issue: 9 Pages: 9558-9565

Resolving the Conformational Dynamics of DNA with Ångstrom Resolution by Pulsed Electron-Electron Double Resonance and Molecular Dynamics.
Journal of the American Chemical Society
Stelzl LS, Erlenbach N, Heinz M, Prisner TF, Hummer G PubMed
Aug 2017 Volume: 139 Issue: 34 Pages: 11674-11677

Activation of the Unfolded Protein Response by Lipid Bilayer Stress.
Molecular cell
Halbleib K, Pesek K, Covino R, Hofbauer HF, Wunnicke D, Hänelt I, Hummer G, Ernst R PubMed
Aug 2017 Volume: 67 Issue: 4 Pages: 673-684.e8

Kinetics from Replica Exchange Molecular Dynamics Simulations.
Journal of chemical theory and computation
Stelzl LS, Hummer G PubMed
Aug 2017 Volume: 13 Issue: 8 Pages: 3927-3935

Intrinsic map dynamics exploration for uncharted effective free-energy landscapes.
Proceedings of the National Academy of Sciences of the United States of America
Chiavazzo E, Covino R, Coifman RR, Gear CW, Georgiou AS, Hummer G, Kevrekidis IG PubMed
Jul 2017 Volume: 114 Issue: 28 Pages: E5494-E5503

Helical jackknives control the gates of the double-pore K uptake system KtrAB.
eLife
Diskowski M, Mehdipour AR, Wunnicke D, Mills DJ, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I PubMed
May 2017 Volume: 6 Issue: Pages:

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis.
eLife
Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A PubMed
May 2017 Volume: 6 Issue: Pages:

Position-Dependent Diffusion Tensors in Anisotropic Media from Simulation: Oxygen Transport in and through Membranes.
Journal of chemical theory and computation
Ghysels A, Venable RM, Pastor RW, Hummer G PubMed
Jun 2017 Volume: 13 Issue: 6 Pages: 2962-2976

Molecule Counts in Localization Microscopy with Organic Fluorophores.
Chemphyschem : a European journal of chemical physics and physical chemistry
Karathanasis C, Fricke F, Hummer G, Heilemann M PubMed
Apr 2017 Volume: 18 Issue: 8 Pages: 942-948

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.
The journal of physical chemistry. A
Simonson T, Hummer G, Roux B PubMed
Feb 2017 Volume: 121 Issue: 7 Pages: 1525-1530

Carbon Nanotubes Mediate Fusion of Lipid Vesicles.
ACS nano
Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G PubMed
Feb 2017 Volume: 11 Issue: 2 Pages: 1273-1280

Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP.
Proceedings of the National Academy of Sciences of the United States of America
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 PubMed
Jan 2017 Volume: 114 Issue: 4 Pages: E438-E447

Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints.
Proteins
Reichel K, Fisette O, Braun T, Lange OF, Hummer G, Schäfer LV PubMed
May 2017 Volume: 85 Issue: 5 Pages: 812-826

Model-independent counting of molecules in single-molecule localization microscopy.
Molecular biology of the cell
Hummer G, Fricke F, Heilemann M PubMed
Nov 2016 Volume: 27 Issue: 22 Pages: 3637-3644

Dynamics of the Orientational Factor in Fluorescence Resonance Energy Transfer.
The journal of physical chemistry. B
Hummer G, Szabo A PubMed
Apr 2017 Volume: 121 Issue: 15 Pages: 3331-3339

Antigenic Peptide Recognition on the Human ABC Transporter TAP Resolved by DNP-Enhanced Solid-State NMR Spectroscopy.
Journal of the American Chemical Society
Lehnert E, Mao J, Mehdipour AR, Hummer G, Abele R, Glaubitz C, Tampé R PubMed
Oct 2016 Volume: 138 Issue: 42 Pages: 13967-13974

Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy.
Biophysical journal
Cossio P, Hummer G, Szabo A PubMed
Aug 2016 Volume: 111 Issue: 4 Pages: 832-840

Cardiolipin puts the seal on ATP synthase.
Proceedings of the National Academy of Sciences of the United States of America
Mehdipour AR, Hummer G PubMed
Aug 2016 Volume: 113 Issue: 31 Pages: 8568-70

Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes.
The journal of physical chemistry. B
Vögele M, Hummer G PubMed
Aug 2016 Volume: 120 Issue: 33 Pages: 8722-32

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers.
The journal of physical chemistry letters
Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV PubMed
Jul 2016 Volume: 7 Issue: 14 Pages: 2676-82

A Eukaryotic Sensor for Membrane Lipid Saturation.
Molecular cell
Covino R, Ballweg S, Stordeur C, Michaelis JB, Puth K, Wernig F, Bahrami A, Ernst AM, Hummer G, Ernst R PubMed
Jul 2016 Volume: 63 Issue: 1 Pages: 49-59

F1-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements.
Proceedings of the National Academy of Sciences of the United States of America
Sugawa M, Okazaki K, Kobayashi M, Matsui T, Hummer G, Masaike T, Nishizaka T PubMed
May 2016 Volume: 113 Issue: 21 Pages: E2916-24

Microscopic interpretation of folding ϕ-values using the transition path ensemble.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
Mar 2016 Volume: 113 Issue: 12 Pages: 3263-8

Molecular simulation and modeling of complex I.
Biochimica et biophysica acta
Hummer G, Wikström M PubMed
Jul 2016 Volume: 1857 Issue: 7 Pages: 915-21

Bayesian ensemble refinement by replica simulations and reweighting.
The Journal of chemical physics
Hummer G, Köfinger J PubMed
Dec 2015 Volume: 143 Issue: 24 Pages: 243150

Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch.
Scientific reports
Blees A, Reichel K, Trowitzsch S, Fisette O, Bock C, Abele R, Hummer G, Schäfer LV, Tampé R PubMed
Nov 2015 Volume: 5 Issue: Pages: 17341

Free energies from dynamic weighted histogram analysis using unbiased Markov state model.
Journal of chemical theory and computation
Rosta E, Hummer G PubMed
Jan 2015 Volume: 11 Issue: 1 Pages: 276-85

On artifacts in single-molecule force spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America
Cossio P, Hummer G, Szabo A PubMed
Nov 2015 Volume: 112 Issue: 46 Pages: 14248-53

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Science (New York, N.Y.)
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, Burghardt I, Hummer G, Boutet S, Schlichting I PubMed
Oct 2015 Volume: 350 Issue: 6259 Pages: 445-50

Redox-induced activation of the proton pump in the respiratory complex I.
Proceedings of the National Academy of Sciences of the United States of America
Sharma V, Belevich G, Gamiz-Hernandez AP, Róg T, Vattulainen I, Verkhovskaya ML, Wikström M, Hummer G, Kaila VR PubMed
Sep 2015 Volume: 112 Issue: 37 Pages: 11571-6

Elasticity, friction, and pathway of γ-subunit rotation in FoF1-ATP synthase.
Proceedings of the National Academy of Sciences of the United States of America
Okazaki K, Hummer G PubMed
Aug 2015 Volume: 112 Issue: 34 Pages: 10720-5

MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data.
Journal of biomolecular NMR
Mantsyzov AB, Shen Y, Lee JH, Hummer G, Bax A PubMed
Sep 2015 Volume: 63 Issue: 1 Pages: 85-95

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Structure (London, England : 1993)
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, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD PubMed
Jul 2015 Volume: 23 Issue: 7 Pages: 1156-67

Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems.
Physical review. X
Johnson ME, Hummer G PubMed
2014 Volume: 4 Issue: 3 Pages:

Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I.
Proceedings of the National Academy of Sciences of the United States of America
Kmita K, Wirth C, Warnau J, Guerrero-Castillo S, Hunte C, Hummer G, Kaila VR, Zwicker K, Brandt U, Zickermann V PubMed
May 2015 Volume: 112 Issue: 18 Pages: 5685-90

Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site.
Structure (London, England : 1993)
Köfinger J, Ragusa MJ, Lee IH, Hummer G, Hurley JH PubMed
May 2015 Volume: 23 Issue: 5 Pages: 809-818

New perspectives on proton pumping in cellular respiration.
Chemical reviews
Wikström M, Sharma V, Kaila VR, Hosler JP, Hummer G PubMed
Mar 2015 Volume: 115 Issue: 5 Pages: 2196-221

Preface: special topic on biological water.
The Journal of chemical physics
Hummer G, Tokmakoff A PubMed
Dec 2014 Volume: 141 Issue: 22 Pages: 22D101

Linear energy relationships in ground state proton transfer and excited state proton-coupled electron transfer.
The journal of physical chemistry. B
Gamiz-Hernandez AP, Magomedov A, Hummer G, Kaila VR PubMed
Feb 2015 Volume: 119 Issue: 6 Pages: 2611-9

Biochemistry. Potassium ions line up.
Science (New York, N.Y.)
Hummer G PubMed
Oct 2014 Volume: 346 Issue: 6207 Pages: 303

Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models.
The journal of physical chemistry. B
Hummer G, Szabo A PubMed
Jul 2015 Volume: 119 Issue: 29 Pages: 9029-37

Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.
The Journal of chemical physics
Nedialkova LV, Amat MA, Kevrekidis IG, Hummer G PubMed
Sep 2014 Volume: 141 Issue: 11 Pages: 114102

A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein.
Protein science : a publication of the Protein Society
Mantsyzov AB, Maltsev AS, Ying J, Shen Y, Hummer G, Bax A PubMed
Sep 2014 Volume: 23 Issue: 9 Pages: 1275-90

Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I.
Proceedings of the National Academy of Sciences of the United States of America
Kaila VR, Wikström M, Hummer G PubMed
May 2014 Volume: 111 Issue: 19 Pages: 6988-93

Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein.
Nature chemistry
Kaila VR, Schotte F, Cho HS, Hummer G, Anfinrud PA PubMed
Apr 2014 Volume: 6 Issue: 4 Pages: 258-9

Calcium inhibition of ribonuclease H1 two-metal ion catalysis.
Journal of the American Chemical Society
Rosta E, Yang W, Hummer G PubMed
Feb 2014 Volume: 136 Issue: 8 Pages: 3137-44

Nobel 2013 Chemistry: Methods for computational chemistry.
Nature
Thiel W, Hummer G PubMed
Dec 2013 Volume: 504 Issue: 7478 Pages: 96-7

Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.
Journal of structural biology
Cossio P, Hummer G PubMed
Dec 2013 Volume: 184 Issue: 3 Pages: 427-37

Native contacts determine protein folding mechanisms in atomistic simulations.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G, Eaton WA PubMed
Oct 2013 Volume: 110 Issue: 44 Pages: 17874-9

Phosphate release coupled to rotary motion of F1-ATPase.
Proceedings of the National Academy of Sciences of the United States of America
Okazaki K, Hummer G PubMed
Oct 2013 Volume: 110 Issue: 41 Pages: 16468-73

Atomic-resolution structural information from scattering experiments on macromolecules in solution.
Physical review. E, Statistical, nonlinear, and soft matter physics
Köfinger J, Hummer G PubMed
May 2013 Volume: 87 Issue: 5 Pages: 052712

Evolutionary pressure on the topology of protein interface interaction networks.
The journal of physical chemistry. B
Johnson ME, Hummer G PubMed
Oct 2013 Volume: 117 Issue: 42 Pages: 13098-106

Interface-resolved network of protein-protein interactions.
PLoS computational biology
Johnson ME, Hummer G PubMed
2013 Volume: 9 Issue: 5 Pages: e1003065

The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin.
PLoS biology
Grigoriu S, Bond R, Cossio P, Chen JA, Ly N, Hummer G, Page R, Cyert MS, Peti W PubMed
2013 Volume: 11 Issue: 2 Pages: e1001492

Theory and simulation of ion conduction in the pentameric GLIC channel.
Journal of chemical theory and computation
Zhu F, Hummer G PubMed
Oct 2012 Volume: 8 Issue: 10 Pages: 3759-3768

Theoretical study of the mechanism of the hydride transfer between ferredoxin-NADP+ reductase and NADP+: the role of Tyr303.
Journal of the American Chemical Society
Lans I, Medina M, Rosta E, Hummer G, Garcia-Viloca M, Lluch JM, González-Lafont À PubMed
Dec 2012 Volume: 134 Issue: 50 Pages: 20544-53

Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography.
Proceedings of the National Academy of Sciences of the United States of America
Schotte F, Cho HS, Kaila VR, Kamikubo H, Dashdorj N, Henry ER, Graber TJ, Henning R, Wulff M, Hummer G, Kataoka M, Anfinrud PA PubMed
Nov 2012 Volume: 109 Issue: 47 Pages: 19256-61

Membrane-elasticity model of Coatless vesicle budding induced by ESCRT complexes.
PLoS computational biology
Różycki B, Boura E, Hurley JH, Hummer G PubMed
2012 Volume: 8 Issue: 10 Pages: e1002736

Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction.
Biophysical journal
Zhu F, Hummer G PubMed
Jul 2012 Volume: 103 Issue: 2 Pages: 219-27

Entropy of single-file water in (6,6) carbon nanotubes.
The Journal of chemical physics
Waghe A, Rasaiah JC, Hummer G PubMed
Jul 2012 Volume: 137 Issue: 4 Pages: 044709

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids.
The Journal of chemical physics
Mittal J, Hummer G PubMed
Jul 2012 Volume: 137 Issue: 3 Pages: 034110

Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.
The journal of physical chemistry. B
Johnson ME, Hummer G PubMed
Jul 2012 Volume: 116 Issue: 29 Pages: 8573-83

Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission.
Structure (London, England : 1993)
Boura E, Różycki B, Chung HS, Herrick DZ, Canagarajah B, Cafiso DS, Eaton WA, Hummer G, Hurley JH PubMed
May 2012 Volume: 20 Issue: 5 Pages: 874-86

Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications.
Proceedings of the National Academy of Sciences of the United States of America
Wikström M, Hummer G PubMed
Mar 2012 Volume: 109 Issue: 12 Pages: 4431-6

Convergence and error estimation in free energy calculations using the weighted histogram analysis method.
Journal of computational chemistry
Zhu F, Hummer G PubMed
Feb 2012 Volume: 33 Issue: 4 Pages: 453-65

Structural basis of p38α regulation by hematopoietic tyrosine phosphatase.
Nature chemical biology
Francis DM, Różycki B, Koveal D, Hummer G, Page R, Peti W PubMed
Nov 2011 Volume: 7 Issue: 12 Pages: 916-24

Energetics of direct and water-mediated proton-coupled electron transfer.
Journal of the American Chemical Society
Kaila VR, Hummer G PubMed
Nov 2011 Volume: 133 Issue: 47 Pages: 19040-3

Resting and active states of the ERK2:HePTP complex.
Journal of the American Chemical Society
Francis DM, Różycki B, Tortajada A, Hummer G, Peti W, Page R PubMed
Nov 2011 Volume: 133 Issue: 43 Pages: 17138-41

Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach.
Biochimica et biophysica acta
Kim YC, Hummer G PubMed
Apr 2012 Volume: 1817 Issue: 4 Pages: 526-36

Diffusion models of protein folding.
Physical chemistry chemical physics : PCCP
Best RB, Hummer G PubMed
Oct 2011 Volume: 13 Issue: 38 Pages: 16902-11

Single-file water in nanopores.
Physical chemistry chemical physics : PCCP
Köfinger J, Hummer G, Dellago C PubMed
Sep 2011 Volume: 13 Issue: 34 Pages: 15403-17

Energetics and dynamics of proton transfer reactions along short water wires.
Physical chemistry chemical physics : PCCP
Kaila VR, Hummer G PubMed
Aug 2011 Volume: 13 Issue: 29 Pages: 13207-15

Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy.
Proceedings of the National Academy of Sciences of the United States of America
Boura E, Rózycki B, Herrick DZ, Chung HS, Vecer J, Eaton WA, Cafiso DS, Hummer G, Hurley JH PubMed
Jun 2011 Volume: 108 Issue: 23 Pages: 9437-42

Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations.
Journal of the American Chemical Society
Rosta E, Nowotny M, Yang W, Hummer G PubMed
Jun 2011 Volume: 133 Issue: 23 Pages: 8934-41

SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions.
Structure (London, England : 1993)
Różycki B, Kim YC, Hummer G PubMed
Jan 2011 Volume: 19 Issue: 1 Pages: 109-16

Crystal structure and allosteric activation of protein kinase C βII.
Cell
Leonard TA, Różycki B, Saidi LF, Hummer G, Hurley JH PubMed
Jan 2011 Volume: 144 Issue: 1 Pages: 55-66

Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks.
Proceedings of the National Academy of Sciences of the United States of America
Johnson ME, Hummer G PubMed
Jan 2011 Volume: 108 Issue: 2 Pages: 603-8

Free energy profiles from single-molecule pulling experiments.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G, Szabo A PubMed
Dec 2010 Volume: 107 Issue: 50 Pages: 21441-6

Water in the polar and nonpolar cavities of the protein interleukin-1β.
The journal of physical chemistry. B
Yin H, Feng G, Clore GM, Hummer G, Rasaiah JC PubMed
Dec 2010 Volume: 114 Issue: 49 Pages: 16290-7

Interfacial thermodynamics of confined water near molecularly rough surfaces.
Faraday discussions
Mittal J, Hummer G PubMed
2010 Volume: 146 Issue: Pages: 341-52; discussion 367-93, 395-401

Pore opening and closing of a pentameric ligand-gated ion channel.
Proceedings of the National Academy of Sciences of the United States of America
Zhu F, Hummer G PubMed
Nov 2010 Volume: 107 Issue: 46 Pages: 19814-9

Molecular binding: Under water's influence.
Nature chemistry
Hummer G PubMed
Nov 2010 Volume: 2 Issue: 11 Pages: 906-7

Biological proton pumping in an oscillating electric field.
Physical review letters
Kim YC, Furchtgott LA, Hummer G PubMed
Dec 2009 Volume: 103 Issue: 26 Pages: 268102

Catching a protein in the act.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G PubMed
Feb 2010 Volume: 107 Issue: 6 Pages: 2381-2

Error and efficiency of simulated tempering simulations.
The Journal of chemical physics
Rosta E, Hummer G PubMed
Jan 2010 Volume: 132 Issue: 3 Pages: 034102

Coordinate-dependent diffusion in protein folding.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
Jan 2010 Volume: 107 Issue: 3 Pages: 1088-93

Thermostat artifacts in replica exchange molecular dynamics simulations.
Journal of chemical theory and computation
Rosta E, Buchete NV, Hummer G PubMed
2009 Volume: 5 Issue: 5 Pages: 1393-1399

Error and efficiency of replica exchange molecular dynamics simulations.
The Journal of chemical physics
Rosta E, Hummer G PubMed
Oct 2009 Volume: 131 Issue: 16 Pages: 165102

Gating transition of pentameric ligand-gated ion channels.
Biophysical journal
Zhu F, Hummer G PubMed
Nov 2009 Volume: 97 Issue: 9 Pages: 2456-63

Exploration of effective potential landscapes using coarse reverse integration.
The Journal of chemical physics
Frewen TA, Hummer G, Kevrekidis IG PubMed
Oct 2009 Volume: 131 Issue: 13 Pages: 134104

Kinetic gating of the proton pump in cytochrome c oxidase.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Wikström M, Hummer G PubMed
Aug 2009 Volume: 106 Issue: 33 Pages: 13707-12

Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides.
The journal of physical chemistry. B
Best RB, Hummer G PubMed
Jul 2009 Volume: 113 Issue: 26 Pages: 9004-15

Reactive flux and folding pathways in network models of coarse-grained protein dynamics.
The Journal of chemical physics
Berezhkovskii A, Hummer G, Szabo A PubMed
May 2009 Volume: 130 Issue: 20 Pages: 205102

Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.
Journal of computational chemistry
Rosta E, Woodcock HL, Brooks BR, Hummer G PubMed
Aug 2009 Volume: 30 Issue: 11 Pages: 1634-41

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase.
Biochimica et biophysica acta
Kaila VR, Verkhovsky MI, Hummer G, Wikström M PubMed
Oct 2009 Volume: 1787 Issue: 10 Pages: 1205-14

A one-dimensional dipole lattice model for water in narrow nanopores.
The Journal of chemical physics
Köfinger J, Hummer G, Dellago C PubMed
Apr 2009 Volume: 130 Issue: 15 Pages: 154110

How mitogen-activated protein kinases recognize and phosphorylate their targets: A QM/MM study.
Journal of the American Chemical Society
Turjanski AG, Hummer G, Gutkind JS PubMed
May 2009 Volume: 131 Issue: 17 Pages: 6141-8

Hybrid structural model of the complete human ESCRT-0 complex.
Structure (London, England : 1993)
Ren X, Kloer DP, Kim YC, Ghirlando R, Saidi LF, Hummer G, Hurley JH PubMed
Mar 2009 Volume: 17 Issue: 3 Pages: 406-16

Biochemistry. Unfolding the secrets of calmodulin.
Science (New York, N.Y.)
Best RB, Hummer G PubMed
Jan 2009 Volume: 323 Issue: 5914 Pages: 593-4

Static and dynamic correlations in water at hydrophobic interfaces.
Proceedings of the National Academy of Sciences of the United States of America
Mittal J, Hummer G PubMed
Dec 2008 Volume: 105 Issue: 51 Pages: 20130-5

Theory, analysis, and interpretation of single-molecule force spectroscopy experiments.
Proceedings of the National Academy of Sciences of the United States of America
Dudko OK, Hummer G, Szabo A PubMed
Oct 2008 Volume: 105 Issue: 41 Pages: 15755-60

Macroscopically ordered water in nanopores.
Proceedings of the National Academy of Sciences of the United States of America
Köfinger J, Hummer G, Dellago C PubMed
Sep 2008 Volume: 105 Issue: 36 Pages: 13218-22

Replica exchange simulations of transient encounter complexes in protein-protein association.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Tang C, Clore GM, Hummer G PubMed
Sep 2008 Volume: 105 Issue: 35 Pages: 12855-60

Atomistic insights into rhodopsin activation from a dynamic model.
Journal of the American Chemical Society
Tikhonova IG, Best RB, Engel S, Gershengorn MC, Hummer G, Costanzi S PubMed
Aug 2008 Volume: 130 Issue: 31 Pages: 10141-9

Layering and position-dependent diffusive dynamics of confined fluids.
Physical review letters
Mittal J, Truskett TM, Errington JR, Hummer G PubMed
Apr 2008 Volume: 100 Issue: 14 Pages: 145901

Peptide folding kinetics from replica exchange molecular dynamics.
Physical review. E, Statistical, nonlinear, and soft matter physics
Buchete NV, Hummer G PubMed
Mar 2008 Volume: 77 Issue: 3 Pt 1 Pages: 030902

A tribute to Attila Szabo.
The journal of physical chemistry. B
Eaton WA, Hummer G, Zwanzig RW PubMed
May 2008 Volume: 112 Issue: 19 Pages: 5881-91

Are current molecular dynamics force fields too helical?
Biophysical journal
Best RB, Buchete NV, Hummer G PubMed
Jul 2008 Volume: 95 Issue: 1 Pages: L07-9

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase.
Proceedings of the National Academy of Sciences of the United States of America
Kaila VR, Verkhovsky MI, Hummer G, Wikström M PubMed
Apr 2008 Volume: 105 Issue: 17 Pages: 6255-9

Prevention of leak in the proton pump of cytochrome c oxidase.
Biochimica et biophysica acta
Kaila VR, Verkhovsky M, Hummer G, Wikström M PubMed
2008 Volume: 1777 Issue: 7-8 Pages: 890-2

Binding-induced folding of a natively unstructured transcription factor.
PLoS computational biology
Turjanski AG, Gutkind JS, Best RB, Hummer G PubMed
Apr 2008 Volume: 4 Issue: 4 Pages: e1000060

Dynamics of cholesterol exchange in the oxysterol binding protein family.
Journal of molecular biology
Canagarajah BJ, Hummer G, Prinz WA, Hurley JH PubMed
May 2008 Volume: 378 Issue: 3 Pages: 737-48

Protein folding kinetics under force from molecular simulation.
Journal of the American Chemical Society
Best RB, Hummer G PubMed
Mar 2008 Volume: 130 Issue: 12 Pages: 3706-7

Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules.
The journal of physical chemistry. B
Best RB, Paci E, Hummer G, Dudko OK PubMed
May 2008 Volume: 112 Issue: 19 Pages: 5968-76

Coarse master equations for peptide folding dynamics.
The journal of physical chemistry. B
Buchete NV, Hummer G PubMed
May 2008 Volume: 112 Issue: 19 Pages: 6057-69

Water in nonpolar confinement: from nanotubes to proteins and beyond.
Annual review of physical chemistry
Rasaiah JC, Garde S, Hummer G PubMed
2008 Volume: 59 Issue: Pages: 713-40

Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding.
Journal of molecular biology
Kim YC, Hummer G PubMed
Feb 2008 Volume: 375 Issue: 5 Pages: 1416-33

Water pulls the strings in hydrophobic polymer collapse.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G PubMed
Sep 2007 Volume: 104 Issue: 38 Pages: 14883-4

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase.
Biochimica et biophysica acta
Tuukkanen A, Kaila VR, Laakkonen L, Hummer G, Wikström M PubMed
Sep 2007 Volume: 1767 Issue: 9 Pages: 1102-6

Protein conformational transitions explored by mixed elastic network models.
Proteins
Zheng W, Brooks BR, Hummer G PubMed
Oct 2007 Volume: 69 Issue: 1 Pages: 43-57

The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting.
Developmental cell
Prag G, Watson H, Kim YC, Beach BM, Ghirlando R, Hummer G, Bonifacino JS, Hurley JH PubMed
Jun 2007 Volume: 12 Issue: 6 Pages: 973-86

Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion.
Journal of the American Chemical Society
Yin H, Hummer G, Rasaiah JC PubMed
Jun 2007 Volume: 129 Issue: 23 Pages: 7369-77

Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins.
Biophysical journal
Dudko OK, Mathé J, Szabo A, Meller A, Hummer G PubMed
Jun 2007 Volume: 92 Issue: 12 Pages: 4188-95

Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils.
Biophysical journal
Buchete NV, Hummer G PubMed
May 2007 Volume: 92 Issue: 9 Pages: 3032-9

Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography.
Journal of molecular biology
Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM PubMed
Mar 2007 Volume: 367 Issue: 3 Pages: 752-63

Slow conformational dynamics and unfolding of the calmodulin C-terminal domain.
Journal of the American Chemical Society
Chen YG, Hummer G PubMed
Mar 2007 Volume: 129 Issue: 9 Pages: 2414-5

Kinetic models of redox-coupled proton pumping.
Proceedings of the National Academy of Sciences of the United States of America
Kim YC, Wikström M, Hummer G PubMed
Feb 2007 Volume: 104 Issue: 7 Pages: 2169-74

Kinetics and mechanism of proton transport across membrane nanopores.
Physical review letters
Dellago C, Hummer G PubMed
Dec 2006 Volume: 97 Issue: 24 Pages: 245901

Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels.
Physical review letters
Berezhkovskii AM, Hummer G, Bezrukov SM PubMed
Jul 2006 Volume: 97 Issue: 2 Pages: 020601

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.
The journal of physical chemistry. B
Sriraman S, Kevrekidis IG, Hummer G PubMed
Apr 2005 Volume: 109 Issue: 14 Pages: 6479-84

Diffusive model of protein folding dynamics with Kramers turnover in rate.
Physical review letters
Best RB, Hummer G PubMed
Jun 2006 Volume: 96 Issue: 22 Pages: 228104

Effects of electric fields on proton transport through water chains.
The Journal of chemical physics
Hassan SA, Hummer G, Lee YS PubMed
May 2006 Volume: 124 Issue: 20 Pages: 204510

Intrinsic rates and activation free energies from single-molecule pulling experiments.
Physical review letters
Dudko OK, Hummer G, Szabo A PubMed
Mar 2006 Volume: 96 Issue: 10 Pages: 108101

Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor.
Structure (London, England : 1993)
Best RB, Chen YG, Hummer G PubMed
Dec 2005 Volume: 13 Issue: 12 Pages: 1755-63

Effect of flexibility on hydrophobic behavior of nanotube water channels.
The Journal of chemical physics
Andreev S, Reichman D, Hummer G PubMed
Nov 2005 Volume: 123 Issue: 19 Pages: 194502

Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.
Proceedings of the National Academy of Sciences of the United States of America
Collins MD, Hummer G, Quillin ML, Matthews BW, Gruner SM PubMed
Nov 2005 Volume: 102 Issue: 46 Pages: 16668-71

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments.
Journal of molecular biology
Buchete NV, Tycko R, Hummer G PubMed
Nov 2005 Volume: 353 Issue: 4 Pages: 804-21

Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes.
Physical review letters
Sriraman S, Kevrekidis IG, Hummer G PubMed
Sep 2005 Volume: 95 Issue: 13 Pages: 130603

Free energy surfaces from single-molecule force spectroscopy.
Accounts of chemical research
Hummer G, Szabo A PubMed
Jul 2005 Volume: 38 Issue: 7 Pages: 504-13

Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations.
Biophysical journal
Peter C, Hummer G PubMed
Oct 2005 Volume: 89 Issue: 4 Pages: 2222-34

Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein".
Science (New York, N.Y.)
Best RB, Hummer G PubMed
Apr 2005 Volume: 308 Issue: 5721 Pages: 498; author reply 498

Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV.
Journal of medicinal chemistry
Gustchina E, Hummer G, Bewley CA, Clore GM PubMed
Apr 2005 Volume: 48 Issue: 8 Pages: 3036-44

Reaction coordinates and rates from transition paths.
Proceedings of the National Academy of Sciences of the United States of America
Best RB, Hummer G PubMed
May 2005 Volume: 102 Issue: 19 Pages: 6732-7

Water clusters in nonpolar cavities.
Proceedings of the National Academy of Sciences of the United States of America
Vaitheeswaran S, Yin H, Rasaiah JC, Hummer G PubMed
Dec 2004 Volume: 101 Issue: 49 Pages: 17002-5

Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations.
Proceedings of the National Academy of Sciences of the United States of America
Hummer G, Schotte F, Anfinrud PA PubMed
Oct 2004 Volume: 101 Issue: 43 Pages: 15330-4

Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes.
The Journal of chemical physics
Vaitheeswaran S, Rasaiah JC, Hummer G PubMed
Oct 2004 Volume: 121 Issue: 16 Pages: 7955-65

Nucleic acid transport through carbon nanotube membranes.
Proceedings of the National Academy of Sciences of the United States of America
Yeh IC, Hummer G PubMed
Aug 2004 Volume: 101 Issue: 33 Pages: 12177-82

From transition paths to transition states and rate coefficients.
The Journal of chemical physics
Hummer G PubMed
Jan 2004 Volume: 120 Issue: 2 Pages: 516-23

Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases.
Biophysical journal
Zweckstetter M, Hummer G, Bax A PubMed
Jun 2004 Volume: 86 Issue: 6 Pages: 3444-60

Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations.
Biophysical journal
Yeh IC, Hummer G PubMed
Feb 2004 Volume: 86 Issue: 2 Pages: 681-9

Osmotic water transport through carbon nanotube membranes.
Proceedings of the National Academy of Sciences of the United States of America
Kalra A, Garde S, Hummer G PubMed
Sep 2003 Volume: 100 Issue: 18 Pages: 10175-80

Kinetics from nonequilibrium single-molecule pulling experiments.
Biophysical journal
Hummer G, Szabo A PubMed
Jul 2003 Volume: 85 Issue: 1 Pages: 5-15

Water-gated mechanism of proton translocation by cytochrome c oxidase.
Biochimica et biophysica acta
Wikström M, Verkhovsky MI, Hummer G PubMed
Jun 2003 Volume: 1604 Issue: 2 Pages: 61-5

Proton transport through water-filled carbon nanotubes.
Physical review letters
Dellago C, Naor MM, Hummer G PubMed
Mar 2003 Volume: 90 Issue: 10 Pages: 105902

Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam.
Journal of the American Chemical Society
Taraphder S, Hummer G PubMed
Apr 2003 Volume: 125 Issue: 13 Pages: 3931-40

Single-file transport of water molecules through a carbon nanotube.
Physical review letters
Berezhkovskii A, Hummer G PubMed
Aug 2002 Volume: 89 Issue: 6 Pages: 064503

Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent.
Journal of the American Chemical Society
Yeh IC, Hummer G PubMed
Jun 2002 Volume: 124 Issue: 23 Pages: 6563-8

Hydrophobicity maps of the N-peptide coiled coil of HIV-1 gp41.
Biochemistry
Siebert X, Hummer G PubMed
Mar 2002 Volume: 41 Issue: 9 Pages: 2956-61