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CHARMM36m: an improved force field for folded and intrinsically disordered proteins

J Huang, S Rauscher, G Nawrocki, T Ran, M Feig, BL De Groot, ...

Nature methods 14 (1), 71-73, 2017

Mandaatit: US National Science Foundation, US National Institutes of Health

Molecular anatomy of a trafficking organelle

S Takamori, M Holt, K Stenius, EA Lemke, M Grønborg, D Riedel, ...

Cell 127 (4), 831-846, 2006

Mandaatit: German Research Foundation

[HTML] springer.com

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

D Seeliger, BL de Groot

Journal of computer-aided molecular design 24 (5), 417-422, 2010

Mandaatit: German Research Foundation

g_wham A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

JS Hub, BL De Groot, D Van Der Spoel

Journal of chemical theory and computation 6 (12), 3713-3720, 2010

Mandaatit: German Research Foundation

Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment

S Rauscher, V Gapsys, MJ Gajda, M Zweckstetter, BL De Groot, ...

Journal of chemical theory and computation 11 (11), 5513-5524, 2015

Mandaatit: German Research Foundation

[PDF] arxiv.org

More bang for your buck: Improved use of GPU nodes for GROMACS 2018

C Kutzner, S Páll, M Fechner, A Esztermann, BL de Groot, H Grubmüller

Journal of computational chemistry 40 (27), 2418-2431, 2019

Mandaatit: German Research Foundation, European Commission

Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations

RA Böckmann, BL De Groot, S Kakorin, E Neumann, H Grubmüller

Biophysical journal 95 (4), 1837-1850, 2008

Mandaatit: German Research Foundation

Ion permeation in K+ channels occurs by direct Coulomb knock-on

DA Köpfer, C Song, T Gruene, GM Sheldrick, U Zachariae, BL de Groot

Science 346 (6207), 352-355, 2014

Mandaatit: German Research Foundation, Volkswagen Foundation

[PDF] embopress.org

Sequential N‐to C‐terminal SNARE complex assembly drives priming and fusion of secretory vesicles

JB Sørensen, K Wiederhold, EM Müller, I Milosevic, G Nagy, BL de Groot, ...

The EMBO journal 25 (5), 955-966, 2006

Mandaatit: German Research Foundation

[PDF] wiley.com

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

C Kutzner, S Páll, M Fechner, A Esztermann, BL de Groot, H Grubmüller

Journal of computational chemistry 36 (26), 1990-2008, 2015

Mandaatit: German Research Foundation

Predicting free energy changes using structural ensembles

A Benedix, CM Becker, BL de Groot, A Caflisch, RA Böckmann

Nature methods 6 (1), 3-4, 2009

Mandaatit: Swiss National Science Foundation, German Research Foundation

Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail

C Kutzner, H Grubmüller, BL De Groot, U Zachariae

Biophysical journal 101 (4), 809-817, 2011

Mandaatit: US National Institutes of Health

Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge

JS Hub, BL De Groot, H Grubmüller, G Groenhof

Journal of chemical theory and computation 10 (1), 381-390, 2014

Mandaatit: German Research Foundation

Protein thermostability calculations using alchemical free energy simulations

D Seeliger, BL De Groot

Biophysical journal 98 (10), 2309-2316, 2010

Mandaatit: German Research Foundation

[PDF] cell.com

A non-canonical voltage-sensing mechanism controls gating in K2P K+ channels

M Schewe, E Nematian-Ardestani, H Sun, M Musinszki, S Cordeiro, ...

Cell 164 (5), 937-949, 2016

Mandaatit: German Research Foundation, UK Biotechnology and Biological Sciences …

[HTML] rsc.org

Large scale relative protein ligand binding affinities using non-equilibrium alchemy

V Gapsys, L Pérez-Benito, M Aldeghi, D Seeliger, H Van Vlijmen, ...

Chemical Science 11 (4), 1140-1152, 2020

Mandaatit: European Commission

[PDF] rug.nl

Direct knock-on of desolvated ions governs strict ion selectivity in K⁺ channels

W Kopec, DA Köpfer, ON Vickery, AS Bondarenko, TLC Jansen, ...

Nature chemistry 10 (8), 813-820, 2018

Mandaatit: German Research Foundation, UK Biotechnology and Biological Sciences …

[HTML] springer.com

Computational analysis of local membrane properties

V Gapsys, BL de Groot, R Briones

Journal of computer-aided molecular design 27, 845-858, 2013

Mandaatit: German Research Foundation

[HTML] pnas.org

Crystal structure and functional mechanism of a human antimicrobial membrane channel

C Song, C Weichbrodt, ES Salnikov, M Dynowski, BO Forsberg, ...

Proceedings of the National Academy of Sciences 110 (12), 4586-4591, 2013

Mandaatit: German Research Foundation

[PDF] cell.com