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Items: 1 to 50 of 162

1.

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

Kopec W, Rothberg BS, de Groot BL.

Nat Commun. 2019 Nov 26;10(1):5366. doi: 10.1038/s41467-019-13227-w.

2.

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

Elisée E, Gapsys V, Mele N, Chaput L, Selwa E, de Groot BL, Iorga BI.

J Comput Aided Mol Des. 2019 Dec;33(12):1031-1043. doi: 10.1007/s10822-019-00232-w. Epub 2019 Nov 1.

PMID:
31677003
3.

Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches.

Aldeghi M, Gapsys V, de Groot BL.

ACS Cent Sci. 2019 Aug 28;5(8):1468-1474. doi: 10.1021/acscentsci.9b00590. Epub 2019 Aug 13.

4.

The conduction pathway of potassium channels is water free under physiological conditions.

Öster C, Hendriks K, Kopec W, Chevelkov V, Shi C, Michl D, Lange S, Sun H, de Groot BL, Lange A.

Sci Adv. 2019 Jul 31;5(7):eaaw6756. doi: 10.1126/sciadv.aaw6756. eCollection 2019 Jul.

5.

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

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

J Comput Chem. 2019 Oct 15;40(27):2418-2431. doi: 10.1002/jcc.26011. Epub 2019 Jul 1.

PMID:
31260119
6.

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

Gapsys V, de Groot BL.

Elife. 2019 Jun 20;8. pii: e44718. doi: 10.7554/eLife.44718.

7.

Identification of kinetic order parameters for non-equilibrium dynamics.

Paul F, Wu H, Vossel M, de Groot BL, Noé F.

J Chem Phys. 2019 Apr 28;150(16):164120. doi: 10.1063/1.5083627.

PMID:
31042914
8.

Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel.

Song C, de Groot BL, Sansom MSP.

Biophys J. 2019 May 7;116(9):1658-1666. doi: 10.1016/j.bpj.2019.03.033. Epub 2019 Apr 5.

PMID:
31010668
9.

Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation.

Coci EG, Gapsys V, Shur N, Shin-Podskarbi Y, de Groot BL, Miller K, Vockley J, Sondheimer N, Ganetzky R, Freisinger P.

Hum Mutat. 2019 Jun;40(6):816-827. doi: 10.1002/humu.23742. Epub 2019 Apr 13.

PMID:
30870574
10.

A molecular mechanism for transthyretin amyloidogenesis.

Yee AW, Aldeghi M, Blakeley MP, Ostermann A, Mas PJ, Moulin M, de Sanctis D, Bowler MW, Mueller-Dieckmann C, Mitchell EP, Haertlein M, de Groot BL, Boeri Erba E, Forsyth VT.

Nat Commun. 2019 Feb 25;10(1):925. doi: 10.1038/s41467-019-08609-z.

11.

A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels.

Schewe M, Sun H, Mert Ü, Mackenzie A, Pike ACW, Schulz F, Constantin C, Vowinkel KS, Conrad LJ, Kiper AK, Gonzalez W, Musinszki M, Tegtmeier M, Pryde DC, Belabed H, Nazare M, de Groot BL, Decher N, Fakler B, Carpenter EP, Tucker SJ, Baukrowitz T.

Science. 2019 Feb 22;363(6429):875-880. doi: 10.1126/science.aav0569.

PMID:
30792303
12.

Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation.

Aldeghi M, Gapsys V, de Groot BL.

ACS Cent Sci. 2018 Dec 26;4(12):1708-1718. doi: 10.1021/acscentsci.8b00717. Epub 2018 Dec 13.

13.

Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.

Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R.

J Am Chem Soc. 2019 Jan 16;141(2):858-869. doi: 10.1021/jacs.8b09258. Epub 2019 Jan 8.

PMID:
30620186
14.

Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels.

Cordeiro S, Finol-Urdaneta RK, Köpfer D, Markushina A, Song J, French RJ, Kopec W, de Groot BL, Giacobassi MJ, Leavitt LS, Raghuraman S, Teichert RW, Olivera BM, Terlau H.

Proc Natl Acad Sci U S A. 2019 Jan 15;116(3):1059-1064. doi: 10.1073/pnas.1813161116. Epub 2018 Dec 28.

15.

GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations.

Briones R, Blau C, Kutzner C, de Groot BL, Aponte-Santamaría C.

Biophys J. 2019 Jan 8;116(1):4-11. doi: 10.1016/j.bpj.2018.11.3126. Epub 2018 Dec 1.

PMID:
30558883
16.

Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles.

Lutz H, Jaeger V, Weidner T, de Groot BL.

J Chem Theory Comput. 2019 Jan 8;15(1):698-707. doi: 10.1021/acs.jctc.8b00840. Epub 2018 Dec 14.

PMID:
30501134
17.

Accurate Calculation of Free Energy Changes upon Amino Acid Mutation.

Aldeghi M, de Groot BL, Gapsys V.

Methods Mol Biol. 2019;1851:19-47. doi: 10.1007/978-1-4939-8736-8_2.

PMID:
30298390
18.

Quantifying Asymmetry of Multimeric Proteins.

Brennecke JT, de Groot BL.

J Phys Chem A. 2018 Oct 4;122(39):7924-7930. doi: 10.1021/acs.jpca.8b06843. Epub 2018 Sep 19.

PMID:
30189732
19.

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

Kopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot BL, Zachariae U.

Nat Chem. 2018 Aug;10(8):813-820. doi: 10.1038/s41557-018-0105-9. Epub 2018 Jul 20.

PMID:
30030538
20.

Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations.

Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV.

J Chem Theory Comput. 2018 Jul 10;14(7):3397-3408. doi: 10.1021/acs.jctc.7b01109. Epub 2018 Jun 21.

PMID:
29847122
21.

In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways.

Heinz LP, Kopec W, de Groot BL, Fink RHA.

Sci Rep. 2018 May 2;8(1):6886. doi: 10.1038/s41598-018-25061-z.

22.

Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets.

Sabo TM, Gapsys V, Walter KFA, Fenwick RB, Becker S, Salvatella X, de Groot BL, Lee D, Griesinger C.

Methods. 2018 Apr 1;138-139:85-92. doi: 10.1016/j.ymeth.2018.04.007. Epub 2018 Apr 12.

PMID:
29656081
23.

Mechanism of Mechanosensitive Gating of the TREK-2 Potassium Channel.

Brennecke JT, de Groot BL.

Biophys J. 2018 Mar 27;114(6):1336-1343. doi: 10.1016/j.bpj.2018.01.030.

24.

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

Shi C, He Y, Hendriks K, de Groot BL, Cai X, Tian C, Lange A, Sun H.

Nat Commun. 2018 Feb 19;9(1):717. doi: 10.1038/s41467-018-03179-y.

25.

Author Correction: Temperature dependence of protein-water interactions in a gated yeast aquaporin.

Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL.

Sci Rep. 2017 Dec 5;7(1):17201. doi: 10.1038/s41598-017-17040-7.

26.

Alchemical Free Energy Calculations for Nucleotide Mutations in Protein-DNA Complexes.

Gapsys V, de Groot BL.

J Chem Theory Comput. 2017 Dec 12;13(12):6275-6289. doi: 10.1021/acs.jctc.7b00849. Epub 2017 Nov 29.

27.

Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation.

Matthes D, Gapsys V, Griesinger C, de Groot BL.

ACS Chem Neurosci. 2017 Dec 20;8(12):2791-2808. doi: 10.1021/acschemneuro.7b00325. Epub 2017 Sep 28.

28.

Temperature dependence of protein-water interactions in a gated yeast aquaporin.

Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL.

Sci Rep. 2017 Jun 21;7(1):4016. doi: 10.1038/s41598-017-04180-z. Erratum in: Sci Rep. 2017 Dec 5;7(1):17201.

29.

Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy.

Ban D, Smith CA, de Groot BL, Griesinger C, Lee D.

Arch Biochem Biophys. 2017 Aug 15;628:81-91. doi: 10.1016/j.abb.2017.05.016. Epub 2017 May 30. Review.

PMID:
28576576
30.

Gating Charge Calculations by Computational Electrophysiology Simulations.

Machtens JP, Briones R, Alleva C, de Groot BL, Fahlke C.

Biophys J. 2017 Apr 11;112(7):1396-1405. doi: 10.1016/j.bpj.2017.02.016.

31.

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

Briones R, Aponte-Santamaría C, de Groot BL.

Front Physiol. 2017 Mar 2;8:124. doi: 10.3389/fphys.2017.00124. eCollection 2017.

32.

Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0.

Saboe PO, Rapisarda C, Kaptan S, Hsiao YS, Summers SR, De Zorzi R, Dukovski D, Yu J, de Groot BL, Kumar M, Walz T.

Biophys J. 2017 Mar 14;112(5):953-965. doi: 10.1016/j.bpj.2017.01.026.

33.

pmx Webserver: A User Friendly Interface for Alchemistry.

Gapsys V, de Groot BL.

J Chem Inf Model. 2017 Feb 27;57(2):109-114. doi: 10.1021/acs.jcim.6b00498. Epub 2017 Feb 16.

PMID:
28181802
34.

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

Huang J, Rauscher S, Nawrocki G, Ran T, Feig M, de Groot BL, Grubmüller H, MacKerell AD Jr.

Nat Methods. 2017 Jan;14(1):71-73. doi: 10.1038/nmeth.4067. Epub 2016 Nov 7.

35.

Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1.

Briones R, Weichbrodt C, Paltrinieri L, Mey I, Villinger S, Giller K, Lange A, Zweckstetter M, Griesinger C, Becker S, Steinem C, de Groot BL.

Biophys J. 2016 Sep 20;111(6):1223-1234. doi: 10.1016/j.bpj.2016.08.007.

36.

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

Matthes D, Gapsys V, Brennecke JT, de Groot BL.

Sci Rep. 2016 Sep 12;6:33156. doi: 10.1038/srep33156.

37.

Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.

Ilgü H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, Fotiadis D.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10358-63. doi: 10.1073/pnas.1605442113. Epub 2016 Aug 31.

38.

Aquaporin 4 as a NH3 Channel.

Assentoft M, Kaptan S, Schneider HP, Deitmer JW, de Groot BL, MacAulay N.

J Biol Chem. 2016 Sep 2;291(36):19184-95. doi: 10.1074/jbc.M116.740217. Epub 2016 Jul 19.

39.

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

Gapsys V, Michielssens S, Seeliger D, de Groot BL.

Angew Chem Int Ed Engl. 2016 Jun 20;55(26):7364-8. doi: 10.1002/anie.201510054. Epub 2016 Apr 28.

40.

Crystal Structure of an Ammonia-Permeable Aquaporin.

Kirscht A, Kaptan SS, Bienert GP, Chaumont F, Nissen P, de Groot BL, Kjellbom P, Gourdon P, Johanson U.

PLoS Biol. 2016 Mar 30;14(3):e1002411. doi: 10.1371/journal.pbio.1002411. eCollection 2016 Mar.

41.

Allosteric switch regulates protein-protein binding through collective motion.

Smith CA, Ban D, Pratihar S, Giller K, Paulat M, Becker S, Griesinger C, Lee D, de Groot BL.

Proc Natl Acad Sci U S A. 2016 Mar 22;113(12):3269-74. doi: 10.1073/pnas.1519609113. Epub 2016 Mar 9.

42.

A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K(+) Channels.

Schewe M, Nematian-Ardestani E, Sun H, Musinszki M, Cordeiro S, Bucci G, de Groot BL, Tucker SJ, Rapedius M, Baukrowitz T.

Cell. 2016 Feb 25;164(5):937-49. doi: 10.1016/j.cell.2016.02.002.

43.

Insights into the function of ion channels by computational electrophysiology simulations.

Kutzner C, Köpfer DA, Machtens JP, de Groot BL, Song C, Zachariae U.

Biochim Biophys Acta. 2016 Jul;1858(7 Pt B):1741-52. doi: 10.1016/j.bbamem.2016.02.006. Epub 2016 Feb 10. Review.

44.

H95 Is a pH-Dependent Gate in Aquaporin 4.

Kaptan S, Assentoft M, Schneider HP, Fenton RA, Deitmer JW, MacAulay N, de Groot BL.

Structure. 2015 Dec 1;23(12):2309-2318. doi: 10.1016/j.str.2015.08.020. Epub 2015 Nov 12.

45.

Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

Rauscher S, Gapsys V, Gajda MJ, Zweckstetter M, de Groot BL, Grubmüller H.

J Chem Theory Comput. 2015 Nov 10;11(11):5513-24. doi: 10.1021/acs.jctc.5b00736. Epub 2015 Oct 22.

PMID:
26574339
46.

Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings.

Gapsys V, Narayanan RL, Xiang S, de Groot BL, Zweckstetter M.

J Biomol NMR. 2015 Nov;63(3):299-307. doi: 10.1007/s10858-015-9990-z. Epub 2015 Oct 3.

PMID:
26433382
47.

The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility.

Linser R, Salvi N, Briones R, Rovó P, de Groot BL, Wagner G.

Proc Natl Acad Sci U S A. 2015 Oct 6;112(40):12390-5. doi: 10.1073/pnas.1513782112. Epub 2015 Sep 21.

48.

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

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

J Comput Chem. 2015 Oct 5;36(26):1990-2008. doi: 10.1002/jcc.24030. Epub 2015 Aug 4.

49.

Binding affinities controlled by shifting conformational equilibria: opportunities and limitations.

Michielssens S, de Groot BL, Grubmüller H.

Biophys J. 2015 May 19;108(10):2585-2590. doi: 10.1016/j.bpj.2015.04.012.

50.

Mechanisms of anion conduction by coupled glutamate transporters.

Machtens JP, Kortzak D, Lansche C, Leinenweber A, Kilian P, Begemann B, Zachariae U, Ewers D, de Groot BL, Briones R, Fahlke C.

Cell. 2015 Jan 29;160(3):542-53. doi: 10.1016/j.cell.2014.12.035.

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