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Items: 1 to 50 of 70

1.

Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking.

Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.

Mitochondrion. 2019 Jul 12. pii: S1567-7249(19)30051-0. doi: 10.1016/j.mito.2019.06.010. [Epub ahead of print]

PMID:
31306768
2.

Molecular modelling as the spark for active learning approaches for interdisciplinary biology teaching.

Taly A, Nitti F, Baaden M, Pasquali S.

Interface Focus. 2019 Jun 6;9(3):20180065. doi: 10.1098/rsfs.2018.0065. Epub 2019 Apr 19.

PMID:
31065338
3.

Highlights from the Faraday Discussion on Artificial Water Channels, Glasgow, UK.

Barboiu M, Kumar M, Baaden M, Gale PA, Hinds BJ.

Chem Commun (Camb). 2019 Apr 7;55(27):3853-3858. doi: 10.1039/c9cc90112d. Epub 2019 Mar 14. No abstract available.

PMID:
30869721
4.

Visualizing Biological Membrane Organization and Dynamics.

Baaden M.

J Mol Biol. 2019 May 3;431(10):1889-1919. doi: 10.1016/j.jmb.2019.02.018. Epub 2019 Mar 4. Review.

PMID:
30844404
5.

Biomimetic water channels: general discussion.

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.

Faraday Discuss. 2018 Sep 28;209(0):205-229. doi: 10.1039/c8fd90020e. No abstract available.

PMID:
30225508
6.

Structure and function of natural proteins for water transport: general discussion.

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.

Faraday Discuss. 2018 Sep 28;209(0):83-95. doi: 10.1039/c8fd90019a. No abstract available.

PMID:
30215655
7.

The modelling and enhancement of water hydrodynamics: general discussion.

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.

Faraday Discuss. 2018 Sep 28;209(0):273-285. doi: 10.1039/c8fd90021c. No abstract available.

PMID:
30215654
8.

Applications to water transport systems: general discussion.

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.

Faraday Discuss. 2018 Sep 28;209(0):389-414. doi: 10.1039/c8fd90022a. No abstract available.

PMID:
30215649
9.

Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.

Esque J, Sansom MSP, Baaden M, Oguey C.

Sci Rep. 2018 Sep 10;8(1):13540. doi: 10.1038/s41598-018-31422-5.

10.

The major β-catenin/E-cadherin junctional binding site is a primary molecular mechano-transductor of differentiation in vivo.

Röper JC, Mitrossilis D, Stirnemann G, Waharte F, Brito I, Fernandez-Sanchez ME, Baaden M, Salamero J, Farge E.

Elife. 2018 Jul 19;7. pii: e33381. doi: 10.7554/eLife.33381.

11.

From Virtual Reality to Immersive Analytics in Bioinformatics.

Sommer B, Baaden M, Krone M, Woods A.

J Integr Bioinform. 2018 Jul 9;15(2). pii: /j/jib.2018.15.issue-2/jib-2018-0043/jib-2018-0043.xml. doi: 10.1515/jib-2018-0043.

12.

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.

Trellet M, Férey N, Flotyński J, Baaden M, Bourdot P.

J Integr Bioinform. 2018 Jul 9;15(2). pii: /j/jib.2018.15.issue-2/jib-2018-0004/jib-2018-0004.xml. doi: 10.1515/jib-2018-0004.

13.

Water permeation across artificial I-quartet membrane channels: from structure to disorder.

Murail S, Vasiliu T, Neamtu A, Barboiu M, Sterpone F, Baaden M.

Faraday Discuss. 2018 Sep 28;209(0):125-148. doi: 10.1039/c8fd00046h.

PMID:
29974103
14.

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.

Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M.

J Integr Bioinform. 2018 Jun 21;15(2). pii: /j/jib.2018.15.issue-2/jib-2018-0006/jib-2018-0006.xml. doi: 10.1515/jib-2018-0006.

15.

Oriented chiral water wires in artificial transmembrane channels.

Kocsis I, Sorci M, Vanselous H, Murail S, Sanders SE, Licsandru E, Legrand YM, van der Lee A, Baaden M, Petersen PB, Belfort G, Barboiu M.

Sci Adv. 2018 Mar 23;4(3):eaao5603. doi: 10.1126/sciadv.aao5603. eCollection 2018 Mar.

16.

Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions.

Delalande O, Molza AE, Dos Santos Morais R, Chéron A, Pollet É, Raguenes-Nicol C, Tascon C, Giudice E, Guilbaud M, Nicolas A, Bondon A, Leturcq F, Férey N, Baaden M, Perez J, Roblin P, Piétri-Rouxel F, Hubert JF, Czjzek M, Le Rumeur E.

J Biol Chem. 2018 May 4;293(18):6637-6646. doi: 10.1074/jbc.M117.809798. Epub 2018 Mar 13.

17.

Ten simple rules to create a serious game, illustrated with examples from structural biology.

Baaden M, Delalande O, Ferey N, Pasquali S, Waldispühl J, Taly A.

PLoS Comput Biol. 2018 Mar 8;14(3):e1005955. doi: 10.1371/journal.pcbi.1005955. eCollection 2018 Mar. No abstract available.

18.

Holding the Nucleosome Together: A Quantitative Description of the DNA-Histone Interface in Solution.

Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C.

J Chem Theory Comput. 2018 Feb 13;14(2):1045-1058. doi: 10.1021/acs.jctc.7b00936. Epub 2018 Jan 8.

PMID:
29262675
19.

Multi-scale simulations of biological systems using the OPEP coarse-grained model.

Sterpone F, Doutreligne S, Tran TT, Melchionna S, Baaden M, Nguyen PH, Derreumaux P.

Biochem Biophys Res Commun. 2018 Mar 29;498(2):296-304. doi: 10.1016/j.bbrc.2017.08.165. Epub 2017 Sep 14.

PMID:
28917842
20.

A membrane-inserted structural model of the yeast mitofusin Fzo1.

De Vecchis D, Cavellini L, Baaden M, Hénin J, Cohen MM, Taly A.

Sci Rep. 2017 Aug 31;7(1):10217. doi: 10.1038/s41598-017-10687-2.

21.

What Can Human-Guided Simulations Bring to RNA Folding?

Mazzanti L, Doutreligne S, Gageat C, Derreumaux P, Taly A, Baaden M, Pasquali S.

Biophys J. 2017 Jul 25;113(2):302-312. doi: 10.1016/j.bpj.2017.05.047. Epub 2017 Jun 22.

22.

Residues of Alpha Helix H3 Determine Distinctive Features of Transforming Growth Factor β3.

Nayeem SM, Oteri F, Baaden M, Deep S.

J Phys Chem B. 2017 Jun 8;121(22):5483-5498. doi: 10.1021/acs.jpcb.7b01867. Epub 2017 May 24.

PMID:
28497965
23.

String method solution of the gating pathways for a pentameric ligand-gated ion channel.

Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4158-E4167. doi: 10.1073/pnas.1617567114. Epub 2017 May 9.

24.

Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation.

Licsandru E, Kocsis I, Shen YX, Murail S, Legrand YM, van der Lee A, Tsai D, Baaden M, Kumar M, Barboiu M.

J Am Chem Soc. 2016 Apr 27;138(16):5403-9. doi: 10.1021/jacs.6b01811. Epub 2016 Apr 18.

PMID:
27063409
25.

Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel.

Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M.

Structure. 2016 Apr 5;24(4):595-605. doi: 10.1016/j.str.2016.02.014. Epub 2016 Mar 24.

26.

Taming molecular flexibility to tackle rare diseases.

Cubellis MV, Baaden M, Andreotti G.

Biochimie. 2015 Jun;113:54-8. doi: 10.1016/j.biochi.2015.03.018. Epub 2015 Apr 2.

27.

Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.

Moraga-Cid G, Sauguet L, Huon C, Malherbe L, Girard-Blanc C, Petres S, Murail S, Taly A, Baaden M, Delarue M, Corringer PJ.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2865-70. doi: 10.1073/pnas.1417864112. Epub 2015 Feb 17.

28.

Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion.

Reddy T, Shorthouse D, Parton DL, Jefferys E, Fowler PW, Chavent M, Baaden M, Sansom MSP.

Structure. 2015 Mar 3;23(3):584-597. doi: 10.1016/j.str.2014.12.019. Epub 2015 Feb 19.

29.

Epock: rapid analysis of protein pocket dynamics.

Laurent B, Chavent M, Cragnolini T, Dahl AC, Pasquali S, Derreumaux P, Sansom MS, Baaden M.

Bioinformatics. 2015 May 1;31(9):1478-80. doi: 10.1093/bioinformatics/btu822. Epub 2014 Dec 12.

30.

Three-dimensional representations of complex carbohydrates and polysaccharides--SweetUnityMol: a video game-based computer graphic software.

Pérez S, Tubiana T, Imberty A, Baaden M.

Glycobiology. 2015 May;25(5):483-91. doi: 10.1093/glycob/cwu133. Epub 2014 Dec 4.

PMID:
25475093
31.

Multiscale simulations give insight into the hydrogen in and out pathways of [NiFe]-hydrogenases from Aquifex aeolicus and Desulfovibrio fructosovorans.

Oteri F, Baaden M, Lojou E, Sacquin-Mora S.

J Phys Chem B. 2014 Dec 4;118(48):13800-11. doi: 10.1021/jp5089965. Epub 2014 Nov 21.

PMID:
25399809
32.

ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations.

Dreher M, Prevoteau-Jonquet J, Trellet M, Piuzzi M, Baaden M, Raffin B, Ferey N, Robert S, Limet S.

Faraday Discuss. 2014;169:119-42. doi: 10.1039/c3fd00142c. Epub 2014 Jul 3.

PMID:
25340956
33.

Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly.

Molza AE, Férey N, Czjzek M, Le Rumeur E, Hubert JF, Tek A, Laurent B, Baaden M, Delalande O.

Faraday Discuss. 2014;169:45-62. doi: 10.1039/c3fd00134b. Epub 2014 Jun 20.

34.

Molecular simulations and visualization: introduction and overview.

Hirst JD, Glowacki DR, Baaden M.

Faraday Discuss. 2014;169:9-22. doi: 10.1039/c4fd90024c. Epub 2014 Oct 6.

PMID:
25285906
35.

The weak, fluctuating, dipole moment of membrane-bound hydrogenase from Aquifex aeolicus accounts for its adaptability to charged electrodes.

Oteri F, Ciaccafava A, de Poulpiquet A, Baaden M, Lojou E, Sacquin-Mora S.

Phys Chem Chem Phys. 2014 Jun 21;16(23):11318-22. doi: 10.1039/c4cp00510d.

PMID:
24789038
36.

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P.

Chem Soc Rev. 2014 Jul 7;43(13):4871-93. doi: 10.1039/c4cs00048j. Epub 2014 Apr 23. Review.

37.

A cooperative mechanism of clotrimazoles in P450 revealed by the dissociation picture of clotrimazole from P450.

Wang M, Baaden M, Wang J, Liang Z.

J Chem Inf Model. 2014 Apr 28;54(4):1218-25. doi: 10.1021/ci400660e. Epub 2014 Mar 26.

PMID:
24611729
38.

Coarse-grain modelling of protein-protein interactions.

Baaden M, Marrink SJ.

Curr Opin Struct Biol. 2013 Dec;23(6):878-86. doi: 10.1016/j.sbi.2013.09.004. Epub 2013 Oct 27. Review.

39.

Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations.

Parton DL, Tek A, Baaden M, Sansom MS.

PLoS Comput Biol. 2013 Apr;9(4):e1003034. doi: 10.1371/journal.pcbi.1003034. Epub 2013 Apr 11.

40.

Game on, science - how video game technology may help biologists tackle visualization challenges.

Lv Z, Tek A, Da Silva F, Empereur-mot C, Chavent M, Baaden M.

PLoS One. 2013;8(3):e57990. doi: 10.1371/journal.pone.0057990. Epub 2013 Mar 6.

41.

Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels.

Sauguet L, Poitevin F, Murail S, Van Renterghem C, Moraga-Cid G, Malherbe L, Thompson AW, Koehl P, Corringer PJ, Baaden M, Delarue M.

EMBO J. 2013 Mar 6;32(5):728-41. doi: 10.1038/emboj.2013.17. Epub 2013 Feb 12.

42.

Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk.

Darré L, Tek A, Baaden M, Pantano S.

J Chem Theory Comput. 2012 Oct 9;8(10):3880-94. doi: 10.1021/ct3001816. Epub 2012 Jun 15.

PMID:
26593029
43.

Understanding small biomolecule-biomaterial interactions: a review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces.

Costa D, Garrain PA, Baaden M.

J Biomed Mater Res A. 2013 Apr;101(4):1210-22. doi: 10.1002/jbm.a.34416. Epub 2012 Sep 27. Review.

PMID:
23015529
44.

A locally closed conformation of a bacterial pentameric proton-gated ion channel.

Prevost MS, Sauguet L, Nury H, Van Renterghem C, Huon C, Poitevin F, Baaden M, Delarue M, Corringer PJ.

Nat Struct Mol Biol. 2012 May 13;19(6):642-9. doi: 10.1038/nsmb.2307.

PMID:
22580559
45.

Enzyme closure and nucleotide binding structurally lock guanylate kinase.

Delalande O, Sacquin-Mora S, Baaden M.

Biophys J. 2011 Sep 21;101(6):1440-9. doi: 10.1016/j.bpj.2011.07.048. Epub 2011 Sep 20.

46.

GPU-accelerated atom and dynamic bond visualization using hyperballs: a unified algorithm for balls, sticks, and hyperboloids.

Chavent M, Vanel A, Tek A, Levy B, Robert S, Raffin B, Baaden M.

J Comput Chem. 2011 Oct;32(13):2924-35. doi: 10.1002/jcc.21861. Epub 2011 Jul 7.

PMID:
21735559
47.
48.

GPU-powered tools boost molecular visualization.

Chavent M, Lévy B, Krone M, Bidmon K, Nominé JP, Ertl T, Baaden M.

Brief Bioinform. 2011 Nov;12(6):689-701. doi: 10.1093/bib/bbq089. Epub 2011 Feb 9.

PMID:
21310717
49.

X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel.

Nury H, Van Renterghem C, Weng Y, Tran A, Baaden M, Dufresne V, Changeux JP, Sonner JM, Delarue M, Corringer PJ.

Nature. 2011 Jan 20;469(7330):428-31. doi: 10.1038/nature09647.

PMID:
21248852
50.

How cations can assist DNase I in DNA binding and hydrolysis.

Guéroult M, Picot D, Abi-Ghanem J, Hartmann B, Baaden M.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001000. doi: 10.1371/journal.pcbi.1001000.

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