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Items: 32

1.

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers.

Schroer CFE, Baldauf L, van Buren L, Wassenaar TA, Melo MN, Koenderink GH, Marrink SJ.

Proc Natl Acad Sci U S A. 2020 Mar 17;117(11):5861-5872. doi: 10.1073/pnas.1914884117. Epub 2020 Mar 2.

2.

LION/web: a web-based ontology enrichment tool for lipidomic data analysis.

Molenaar MR, Jeucken A, Wassenaar TA, van de Lest CHA, Brouwers JF, Helms JB.

Gigascience. 2019 Jun 1;8(6). pii: giz061. doi: 10.1093/gigascience/giz061.

3.

Statistical efficiency of methods for computing free energy of hydration.

Yildirim A, Wassenaar TA, van der Spoel D.

J Chem Phys. 2018 Oct 14;149(14):144111. doi: 10.1063/1.5041835.

PMID:
30316276
4.

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins.

Corradi V, Mendez-Villuendas E, Ingólfsson HI, Gu RX, Siuda I, Melo MN, Moussatova A, DeGagné LJ, Sejdiu BI, Singh G, Wassenaar TA, Delgado Magnero K, Marrink SJ, Tieleman DP.

ACS Cent Sci. 2018 Jun 27;4(6):709-717. doi: 10.1021/acscentsci.8b00143. Epub 2018 Jun 13.

5.

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain.

Jayaraman K, Morley AN, Szöllősi D, Wassenaar TA, Sitte HH, Stockner T.

PLoS Comput Biol. 2018 Jun 6;14(6):e1006229. doi: 10.1371/journal.pcbi.1006229. eCollection 2018 Jun.

6.

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.

Capoferri L, van Dijk M, Rustenburg AS, Wassenaar TA, Kooi DP, Rifai EA, Vermeulen NPE, Geerke DP.

J Cheminform. 2017 Nov 21;9(1):58. doi: 10.1186/s13321-017-0243-x.

7.

Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4.

Pluhackova K, Gahbauer S, Kranz F, Wassenaar TA, Böckmann RA.

PLoS Comput Biol. 2016 Nov 3;12(11):e1005169. doi: 10.1371/journal.pcbi.1005169. eCollection 2016 Nov.

8.

A MoS2-Based Capacitive Displacement Sensor for DNA Sequencing.

Smolyanitsky A, Yakobson BI, Wassenaar TA, Paulechka E, Kroenlein K.

ACS Nano. 2016 Sep 27;10(9):9009-16. doi: 10.1021/acsnano.6b05274. Epub 2016 Sep 16.

PMID:
27623171
9.

Nucleobase-functionalized graphene nanoribbons for accurate high-speed DNA sequencing.

Paulechka E, Wassenaar TA, Kroenlein K, Kazakov A, Smolyanitsky A.

Nanoscale. 2016 Jan 28;8(4):1861-7. doi: 10.1039/c5nr07061a.

PMID:
26731166
10.

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach.

Wassenaar TA, Pluhackova K, Moussatova A, Sengupta D, Marrink SJ, Tieleman DP, Böckmann RA.

J Chem Theory Comput. 2015 May 12;11(5):2278-91. doi: 10.1021/ct5010092. Epub 2015 Mar 26.

PMID:
26574426
11.

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.

Wassenaar TA, Ingólfsson HI, Böckmann RA, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2015 May 12;11(5):2144-55. doi: 10.1021/acs.jctc.5b00209. Epub 2015 Apr 24.

PMID:
26574417
12.

Synaptobrevin Transmembrane Domain Dimerization Studied by Multiscale Molecular Dynamics Simulations.

Han J, Pluhackova K, Wassenaar TA, Böckmann RA.

Biophys J. 2015 Aug 18;109(4):760-71. doi: 10.1016/j.bpj.2015.06.049.

13.

Molecular dynamics study of the effect of active site protonation on Helicobacter pylori 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

Tekpinar M, Yildirim A, Wassenaar TA.

Eur Biophys J. 2015 Dec;44(8):685-96. doi: 10.1007/s00249-015-1067-0. Epub 2015 Aug 8.

PMID:
26254213
14.

Activation of the bacterial thermosensor DesK involves a serine zipper dimerization motif that is modulated by bilayer thickness.

Cybulski LE, Ballering J, Moussatova A, Inda ME, Vazquez DB, Wassenaar TA, de Mendoza D, Tieleman DP, Killian JA.

Proc Natl Acad Sci U S A. 2015 May 19;112(20):6353-8. doi: 10.1073/pnas.1422446112. Epub 2015 May 4.

15.

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

van Eerden FJ, de Jong DH, de Vries AH, Wassenaar TA, Marrink SJ.

Biochim Biophys Acta. 2015 Jun;1848(6):1319-30. doi: 10.1016/j.bbamem.2015.02.025. Epub 2015 Mar 5.

16.

Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer.

Pluhackova K, Wassenaar TA, Kirsch S, Böckmann RA.

J Phys Chem B. 2015 Mar 26;119(12):4396-408. doi: 10.1021/acs.jpcb.5b00434. Epub 2015 Mar 12.

PMID:
25719673
17.

Thermodynamic and kinetic characterization of transmembrane helix association.

Pawar AB, Deshpande SA, Gopal SM, Wassenaar TA, Athale CA, Sengupta D.

Phys Chem Chem Phys. 2015 Jan 14;17(2):1390-8. doi: 10.1039/c4cp03732d. Epub 2014 Nov 26.

PMID:
25427292
18.

Lipid organization of the plasma membrane.

Ingólfsson HI, Melo MN, van Eerden FJ, Arnarez C, Lopez CA, Wassenaar TA, Periole X, de Vries AH, Tieleman DP, Marrink SJ.

J Am Chem Soc. 2014 Oct 15;136(41):14554-9. doi: 10.1021/ja507832e. Epub 2014 Oct 1.

19.

Molecular dynamics investigation of Helicobacter pylori chemotactic protein CheY1 and two mutants.

Yildirim A, Tekpinar M, Wassenaar TA.

J Mol Model. 2014 Apr;20(4):2212. doi: 10.1007/s00894-014-2212-x. Epub 2014 Apr 3.

PMID:
24696315
20.

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models.

Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP.

J Chem Theory Comput. 2014 Feb 11;10(2):676-90. doi: 10.1021/ct400617g. Epub 2014 Jan 21.

PMID:
26580045
21.

X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes.

Boscia AL, Treece BW, Mohammadyani D, Klein-Seetharaman J, Braun AR, Wassenaar TA, Klösgen B, Tristram-Nagle S.

Chem Phys Lipids. 2014 Feb;178:1-10. doi: 10.1016/j.chemphyslip.2013.12.010. Epub 2013 Dec 28.

22.

The effect of triple glutamic mutations E9Q/E194Q/E204Q on the structural stability of bacteriorhodopsin.

Lazarova T, Mlynarczyk K, Filipek S, Kolinski M, Wassenaar TA, Querol E, Renugopalakrishnan V, Viswanathan S, Padrós E.

FEBS J. 2014 Feb;281(4):1181-95. doi: 10.1111/febs.12694. Epub 2014 Jan 10.

23.

Molecular dynamics simulations of membrane proteins.

Pluhackova K, Wassenaar TA, Böckmann RA.

Methods Mol Biol. 2013;1033:85-101. doi: 10.1007/978-1-62703-487-6_6.

PMID:
23996172
24.

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

Wassenaar TA, Ingólfsson HI, Priess M, Marrink SJ, Schäfer LV.

J Phys Chem B. 2013 Apr 4;117(13):3516-30. doi: 10.1021/jp311533p. Epub 2013 Mar 6.

25.

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

de Jong DH, Singh G, Bennett WF, Arnarez C, Wassenaar TA, Schäfer LV, Periole X, Tieleman DP, Marrink SJ.

J Chem Theory Comput. 2013 Jan 8;9(1):687-97. doi: 10.1021/ct300646g. Epub 2012 Nov 28.

PMID:
26589065
26.

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions.

Wassenaar TA, de Vries S, Bonvin AM, Bekker H.

J Chem Theory Comput. 2012 Oct 9;8(10):3618-27. doi: 10.1021/ct3000662. Epub 2012 Jun 6.

PMID:
26593007
27.

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.

van Dijk M, Wassenaar TA, Bonvin AM.

J Chem Theory Comput. 2012 Oct 9;8(10):3463-72. doi: 10.1021/ct300102d. Epub 2012 Apr 18.

PMID:
26592996
28.

The eNMR platform for structural biology.

Bonvin AM, Rosato A, Wassenaar TA.

J Struct Funct Genomics. 2010 Mar;11(1):1-8. doi: 10.1007/s10969-010-9084-9. Epub 2010 Mar 13.

29.

Calcium binding to the purple membrane: A molecular dynamics study.

Wassenaar TA, Daura X, Padrós E, Mark AE.

Proteins. 2009 Feb 15;74(3):669-81. doi: 10.1002/prot.22182.

PMID:
18704943
31.
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