Works matching AU de Groot, Bert L.

Results: 61

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan.

Published in:

Angewandte Chemie, 2016, v. 128, n. 26, p. 7490, doi. 10.1002/ange.201510054

By:

Gapsys, Vytautas;
Michielssens, Servaas;
Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

Population Shuffling of Protein Conformations.

Published in:

Angewandte Chemie, 2015, v. 127, n. 1, p. 209, doi. 10.1002/ange.201408890

By:

Smith, Colin A.;
Ban, David;
Pratihar, Supriya;
Giller, Karin;
Schwiegk, Claudia;
de Groot, Bert L.;
Becker, Stefan;
Griesinger, Christian;
Lee, Donghan

Publication type:

Article

A Designed Conformational Shift To Control Protein Binding Specificity.

Published in:

Angewandte Chemie, 2014, v. 126, n. 39, p. 10535, doi. 10.1002/ange.201403102

By:

Michielssens, Servaas;
Peters, Jan Henning;
Ban, David;
Pratihar, Supriya;
Seeliger, Daniel;
Sharma, Monika;
Giller, Karin;
Sabo, Thomas Michael;
Becker, Stefan;
Lee, Donghan;
Griesinger, Christian;
de Groot, Bert L.

Publication type:

Article

Kinetics of Conformational Sampling in Ubiquitin.

Published in:

Angewandte Chemie, 2011, v. 123, n. 48, p. 11639, doi. 10.1002/ange.201105086

By:

Ban, David;
Funk, Michael;
Gulich, Rudolf;
Egger, Dalia;
Sabo, T. Michael;
Walter, Korvin F. A.;
Fenwick, R. Bryn;
Giller, Karin;
Pichierri, Fabio;
de Groot, Bert L.;
Lange, Oliver F.;
Grubmüller, Helmut;
Salvatella, Xavier;
Wolf, Martin;
Loidl, Alois;
Kree, Reiner;
Becker, Stefan;
Lakomek, Nils-Alexander;
Lee, Donghan;
Lunkenheimer, Peter

Publication type:

Article

The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction.

Published in:

Angewandte Chemie International Edition, 2009, v. 48, n. 28, p. 5207, doi. 10.1002/anie.200900481

By:

Stegmann, Christian M.;
Seeliger, Daniel;
Sheldrick, George M.;
de Groot, Bert L.;
Wahl, Markus C.

Publication type:

Article

Molecular Dynamics Simulations of Protein G Challenge NMR-Derived Correlated Backbone MotionsWe thank Christian Griesinger, Sander Nabuurs, and Martin Stone for carefully reading the manuscript.

Published in:

Angewandte Chemie International Edition, 2005, v. 44, n. 22, p. 3394, doi. 10.1002/anie.200462957

By:

Oliver F. Lange;
Helmut Grubmüller;
Bert L. de Groot

Publication type:

Article

Speeding up parallel GROMACS on high-latency networks.

Published in:

Journal of Computational Chemistry, 2007, v. 28, n. 12, p. 2075, doi. 10.1002/jcc.20703

By:

Kutzner, Carsten;
Van Der Spoel, David;
Fechner, Martin;
Lindahl, Erik;
Schmitt, Udo W.;
De Groot, Bert L.;
Grubmüller, Helmut

Publication type:

Article

Structure, gating and interactions of the voltage-dependent anion channel.

Published in:

European Biophysics Journal, 2021, v. 50, n. 2, p. 159, doi. 10.1007/s00249-021-01515-7

By:

Najbauer, Eszter E.;
Becker, Stefan;
Giller, Karin;
Zweckstetter, Markus;
Lange, Adam;
Steinem, Claudia;
de Groot, Bert L.;
Griesinger, Christian;
Andreas, Loren B.

Publication type:

Article

Lipid–protein forces predict conformational changes in a mechanosensitive channel.

Published in:

European Biophysics Journal, 2021, v. 50, n. 2, p. 181, doi. 10.1007/s00249-020-01488-z

By:

Daday, Csaba;
de Groot, Bert L.

Publication type:

Article

A litmus test for classifying recognition mechanisms of transiently binding proteins.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31374-5

By:

Chakrabarti, Kalyan S.;
Olsson, Simon;
Pratihar, Supriya;
Giller, Karin;
Overkamp, Kerstin;
Lee, Ko On;
Gapsys, Vytautas;
Ryu, Kyoung-Seok;
de Groot, Bert L.;
Noé, Frank;
Becker, Stefan;
Lee, Donghan;
Weikl, Thomas R.;
Griesinger, Christian

Publication type:

Article

A Molecular Switch Driving Inactivation in the Cardiac K<sup>+</sup> Channel hERG.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0041023

By:

Köpfer, David A.;
Hahn, Ulrike;
Ohmert, Iris;
Vriend, Gert;
Pongs, Olaf;
Groot, Bert L. de;
Zachariae, Ulrich

Publication type:

Article

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization.

Published in:

PLoS ONE, 2011, v. 6, n. 5, p. 1, doi. 10.1371/journal.pone.0019129

By:

Matthes, Dirk;
Gapsys, Vytautas;
Daebel, Venita;
de Groot, Bert L.

Publication type:

Article

Enhancing NMR derived ensembles with kinetics on multiple timescales.

Published in:

Journal of Biomolecular NMR, 2020, v. 74, n. 1, p. 27, doi. 10.1007/s10858-019-00288-8

By:

Smith, Colin A.;
Mazur, Adam;
Rout, Ashok K.;
Becker, Stefan;
Lee, Donghan;
de Groot, Bert L.;
Griesinger, Christian

Publication type:

Article

Central cavity dehydration as a gating mechanism of potassium channels.

Published in:

Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-37531-8

By:

Gu, Ruo-Xu;
de Groot, Bert L.

Publication type:

Article

The 3D structure of lipidic fibrils of α-synuclein.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-34552-7

By:

Frieg, Benedikt;
Antonschmidt, Leif;
Dienemann, Christian;
Geraets, James A.;
Najbauer, Eszter E.;
Matthes, Dirk;
de Groot, Bert L.;
Andreas, Loren B.;
Becker, Stefan;
Griesinger, Christian;
Schröder, Gunnar F.

Publication type:

Article

The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-32797-w

By:

Antonschmidt, Leif;
Matthes, Dirk;
Dervişoğlu, Rıza;
Frieg, Benedikt;
Dienemann, Christian;
Leonov, Andrei;
Nimerovsky, Evgeny;
Sant, Vrinda;
Ryazanov, Sergey;
Giese, Armin;
Schröder, Gunnar F.;
Becker, Stefan;
de Groot, Bert L.;
Griesinger, Christian;
Andreas, Loren B.

Publication type:

Article

Crystal Structure of an Ammonia-Permeable Aquaporin.

Published in:

PLoS Biology, 2016, v. 14, n. 3, p. 1, doi. 10.1371/journal.pbio.1002411

By:

Kirscht, Andreas;
Kaptan, Shreyas S.;
Bienert, Gerd Patrick;
Chaumont, François;
Nissen, Poul;
de Groot, Bert L.;
Kjellbom, Per;
Gourdon, Pontus;
Johanson, Urban

Publication type:

Article

An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase.

Published in:

Scientific Reports, 2016, p. 33156, doi. 10.1038/srep33156

By:

Matthes, Dirk;
Gapsys, Vytautas;
Brennecke, Julian T.;
de Groot, Bert L.

Publication type:

Article

A single NaK channel conformation is not enough for non-selective ion conduction.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-03179-y

By:

Chaowei Shi;
Yao He;
Hendriks, Kitty;
de Groot, Bert L.;
Xiaoying Cai;
Changlin Tian;
Lange, Adam;
Han Sun

Publication type:

Article

Domain motions of hyaluronan lyase underlying processive hyaluronan translocation.

Published in:

Proteins, 2009, v. 76, n. 1, p. 30, doi. 10.1002/prot.22316

By:

Joshi, Harshad V.;
Jedrzejas, Mark J.;
de Groot, Bert L.

Publication type:

Article

Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps.

Published in:

Proteins, 2007, v. 68, n. 3, p. 595, doi. 10.1002/prot.21447

By:

Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism.

Published in:

2009

By:

Fischer, Gerhard;
Kosinska-Eriksson, Urszula;
Aponte-Santamaría, Camilo;
Palmgren, Madelene;
Geijer, Cecilia;
Hedfalk, Kristina;
Hohmann, Stefan;
de Groot, Bert L.;
Neutze, Richard;
Lindkvist-Petersson, Karin

Publication type:

Bibliography

Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches.

Published in:

Communications Chemistry, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42004-021-00498-y

By:

Gapsys, Vytautas;
Yildirim, Ahmet;
Aldeghi, Matteo;
Khalak, Yuriy;
van der Spoel, David;
de Groot, Bert L.

Publication type:

Article

Lipid-protein interactions modulate the conformational equilibrium of a potassium channel.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15741-8

By:

Gu, Ruo-Xu;
de Groot, Bert L.

Publication type:

Article

Collective Dynamics Underlying Allosteric Transitions in Hemoglobin.

Published in:

PLoS Computational Biology, 2013, v. 9, n. 9, p. 1, doi. 10.1371/journal.pcbi.1003232

By:

Vesper, Martin D.;
de Groot, Bert L.

Publication type:

Article

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

Published in:

PLoS Computational Biology, 2013, v. 9, n. 5, p. 1, doi. 10.1371/journal.pcbi.1003058

By:

Linder, Tobias;
de Groot, Bert L.;
Stary-Weinzinger, Anna

Publication type:

Article

Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection.

Published in:

PLoS Computational Biology, 2012, v. 8, n. 10, p. 1, doi. 10.1371/journal.pcbi.1002704

By:

Peters, Jan H.;
De Groot, Bert L.

Publication type:

Article

Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 5, p. 1, doi. 10.1371/journal.pcbi.1000774

By:

Hub, Jochen S.;
Kubitzki, Marcus B.;
de Groot, Bert L.

Publication type:

Article

Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1371/journal.pcbi.1000634

By:

Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

Detection of Functional Modes in Protein Dynamics.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000480

By:

Hub, Jochen S.;
de Groot, Bert L.

Publication type:

Article

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations.

Published in:

Journal of Computational Chemistry, 2015, v. 36, n. 26, p. 1990, doi. 10.1002/jcc.24030

By:

Kutzner, Carsten;
Páll, Szilárd;
Fechner, Martin;
Esztermann, Ansgar;
de Groot, Bert L.;
Grubmüller, Helmut

Publication type:

Article

pmx: Automated protein structure and topology generation for alchemical perturbations.

Published in:

Journal of Computational Chemistry, 2015, v. 36, n. 5, p. 348, doi. 10.1002/jcc.23804

By:

Gapsys, Vytautas;
Michielssens, Servaas;
Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules.

Published in:

Journal of Computational Chemistry, 2009, v. 30, n. 7, p. 1160, doi. 10.1002/jcc.21127

By:

SEELIGER, DANIEL;
DE GROOT, BERT L.

Publication type:

Article

Predicting free energy changes using structural ensembles.

Published in:

Nature Methods, 2009, v. 6, n. 1, p. 3, doi. 10.1038/nmeth0109-3

By:

Benedix, Alexander;
Becker, Caroline M.;
de Groot, Bert L.;
Caflisch, Amedeo;
Böckmann, Rainer A.

Publication type:

Article

A Decade of Debate: Significance of CO.

Published in:

ChemPhysChem, 2011, v. 12, n. 5, p. 1021, doi. 10.1002/cphc.201000974

By:

de Groot, Bert L.;
Hub, Jochen S.

Publication type:

Article

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.

Published in:

Journal of Computer-Aided Molecular Design, 2021, v. 35, n. 1, p. 49, doi. 10.1007/s10822-020-00359-1

By:

Khalak, Yuriy;
Tresadern, Gary;
de Groot, Bert L.;
Gapsys, Vytautas

Publication type:

Article

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.

Published in:

Journal of Computer-Aided Molecular Design, 2020, v. 34, n. 5, p. 601, doi. 10.1007/s10822-020-00290-5

By:

Rizzi, Andrea;
Jensen, Travis;
Slochower, David R.;
Aldeghi, Matteo;
Gapsys, Vytautas;
Ntekoumes, Dimitris;
Bosisio, Stefano;
Papadourakis, Michail;
Henriksen, Niel M.;
de Groot, Bert L.;
Cournia, Zoe;
Dickson, Alex;
Michel, Julien;
Gilson, Michael K.;
Shirts, Michael R.;
Mobley, David L.;
Chodera, John D.

Publication type:

Article

Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.

Published in:

Journal of Computer-Aided Molecular Design, 2019, v. 33, n. 12, p. 1031, doi. 10.1007/s10822-019-00232-w

By:

Elisée, Eddy;
Gapsys, Vytautas;
Mele, Nawel;
Chaput, Ludovic;
Selwa, Edithe;
de Groot, Bert L.;
Iorga, Bogdan I.

Publication type:

Article

Computational analysis of local membrane properties.

Published in:

Journal of Computer-Aided Molecular Design, 2013, v. 27, n. 10, p. 845, doi. 10.1007/s10822-013-9684-0

By:

Gapsys, Vytautas;
de Groot, Bert L.;
Briones, Rodolfo

Publication type:

Article

Ligand docking and binding site analysis with PyMOL and Autodock/Vina.

Published in:

Journal of Computer-Aided Molecular Design, 2010, v. 24, n. 5, p. 417, doi. 10.1007/s10822-010-9352-6

By:

Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with <sup>2</sup>H NMR experiments.

Published in:

European Biophysics Journal, 2007, v. 36, n. 8, p. 919, doi. 10.1007/s00249-007-0192-9

By:

Vermeer, Louic S.;
De Groot, Bert L.;
Réat, Valérie;
Milon, Alain;
Czaplicki, Jerzy

Publication type:

Article

Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects.

Published in:

Frontiers in Physiology, 2017, v. 8, p. 1, doi. 10.3389/fphys.2017.00124

By:

Briones, Rodolfo;
Aponte-Santamaría, Camilo;
de Groot, Bert L.

Publication type:

Article

Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.

Published in:

Journal of Computational Chemistry, 2025, v. 46, n. 5, p. 1, doi. 10.1002/jcc.70059

By:

Kutzner, Carsten;
Miletić, Vedran;
Palacio Rodríguez, Karen;
Rampp, Markus;
Hummer, Gerhard;
de Groot, Bert L.;
Grubmüller, Helmut

Publication type:

Article

Resolving coupled pH titrations using alchemical free energy calculations.

Published in:

Journal of Computational Chemistry, 2024, v. 45, n. 17, p. 1444, doi. 10.1002/jcc.27318

By:

Wilson, Carter J.;
de Groot, Bert L.;
Gapsys, Vytautas

Publication type:

Article

Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-13227-w

By:

Kopec, Wojciech;
Rothberg, Brad S.;
de Groot, Bert L.

Publication type:

Article

A molecular mechanism for transthyretin amyloidogenesis.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-08609-z

By:

Yee, Ai Woon;
Aldeghi, Matteo;
Blakeley, Matthew P.;
Ostermann, Andreas;
Mas, Philippe J.;
Moulin, Martine;
de Sanctis, Daniele;
Bowler, Matthew W.;
Mueller-Dieckmann, Christoph;
Mitchell, Edward P.;
Haertlein, Michael;
de Groot, Bert L.;
Boeri Erba, Elisabetta;
Forsyth, V. Trevor

Publication type:

Article

Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan.

Published in:

Angewandte Chemie International Edition, 2016, v. 55, n. 26, p. 7364, doi. 10.1002/anie.201510054

By:

Gapsys, Vytautas;
Michielssens, Servaas;
Seeliger, Daniel;
de Groot, Bert L.

Publication type:

Article

Automated relative binding free energy calculations from SMILES to ΔΔG.

Published in:

Communications Chemistry, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42004-023-00859-9

By:

Moore, J. Harry;
Margreitter, Christian;
Janet, Jon Paul;
Engkvist, Ola;
de Groot, Bert L.;
Gapsys, Vytautas

Publication type:

Article

Structure and dynamics of cholesterolmediated aquaporin-0 arrays and implications for lipid rafts.

Published in:

eLife, 2024, p. 1, doi. 10.7554/eLife.90851

By:

Chiu, Po-Lin;
Orjuela, Juan D.;
de Groot, Bert L.;
Santamaría, Camilo Aponte;
Walz, Thomas

Publication type:

Article

Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors.

Published in:

Retrovirology, 2020, v. 17, n. 1, p. 1, doi. 10.1186/s12977-020-00520-6

By:

Bastys, Tomas;
Gapsys, Vytautas;
Walter, Hauke;
Heger, Eva;
Doncheva, Nadezhda T.;
Kaiser, Rolf;
de Groot, Bert L.;
Kalinina, Olga V.

Publication type:

Article