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Items: 1 to 50 of 56

1.

Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells.

Pitard I, Malliavin TE.

Toxins (Basel). 2019 Jun 24;11(6). pii: E369. doi: 10.3390/toxins11060369. Review.

2.

Minimal NMR distance information for rigidity of protein graphs.

Lavor C, Liberti L, Donald B, Worley B, Bardiaux B, Malliavin TE, Nilges M.

Discrete Appl Math. 2019 Mar 15;256:91-104. doi: 10.1016/j.dam.2018.03.071. Epub 2018 Apr 26.

3.

Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function.

Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE.

PLoS One. 2018 Nov 29;13(11):e0207899. doi: 10.1371/journal.pone.0207899. eCollection 2018.

4.

Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study.

Chiodo L, Malliavin TE, Giuffrida S, Maragliano L, Cottone G.

J Chem Inf Model. 2018 Nov 26;58(11):2278-2293. doi: 10.1021/acs.jcim.8b00412. Epub 2018 Nov 7.

5.

re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling.

Lamothe G, Malliavin TE.

BMC Struct Biol. 2018 Apr 3;18(1):4. doi: 10.1186/s12900-018-0083-6.

6.

A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study.

Chiodo L, Malliavin TE, Maragliano L, Cottone G.

Biophys Chem. 2017 Oct;229:99-109. doi: 10.1016/j.bpc.2017.06.010. Epub 2017 Jun 30.

PMID:
28697974
7.

Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics.

Malliavin TE.

Toxins (Basel). 2017 Jun 26;9(7). pii: E199. doi: 10.3390/toxins9070199. Review.

8.

Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA.

Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE.

J Chem Inf Model. 2016 Sep 26;56(9):1762-75. doi: 10.1021/acs.jcim.6b00211. Epub 2016 Sep 12.

9.

Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA.

Martinez M, Duclert-Savatier N, Betton JM, Alzari PM, Nilges M, Malliavin TE.

Biopolymers. 2016 Oct;105(10):670-82. doi: 10.1002/bip.22864.

PMID:
27124288
10.

Improving the prediction of organism-level toxicity through integration of chemical, protein target and cytotoxicity qHTS data.

Allen CHG, Koutsoukas A, Cortés-Ciriano I, Murrell DS, Malliavin TE, Glen RC, Bender A.

Toxicol Res (Camb). 2016 Mar 3;5(3):883-894. doi: 10.1039/c5tx00406c. eCollection 2016 May 1.

11.

Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information.

Cortes-Ciriano I, Bouvier G, Nilges M, Maragliano L, Malliavin TE.

J Chem Theory Comput. 2015 Jul 14;11(7):3446-54. doi: 10.1021/acs.jctc.5b00153. Epub 2015 Jun 3.

PMID:
26575778
12.

Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel.

Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE.

Bioinformatics. 2016 Jan 1;32(1):85-95. doi: 10.1093/bioinformatics/btv529. Epub 2015 Sep 8.

13.

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC.

J Cheminform. 2015 Aug 28;7:45. doi: 10.1186/s13321-015-0086-2. eCollection 2015.

14.

A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation.

Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G.

PLoS One. 2015 Jul 24;10(7):e0133011. doi: 10.1371/journal.pone.0133011. eCollection 2015.

15.

Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets.

Cortes-Ciriano I, Bender A, Malliavin TE.

J Chem Inf Model. 2015 Jul 27;55(7):1413-25. doi: 10.1021/acs.jcim.5b00101. Epub 2015 Jun 18.

PMID:
26038978
16.

Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules.

Paricharak S, Cortés-Ciriano I, IJzerman AP, Malliavin TE, Bender A.

J Cheminform. 2015 Apr 15;7:15. doi: 10.1186/s13321-015-0063-9. eCollection 2015.

17.

Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis.

Harigua-Souiai E, Cortes-Ciriano I, Desdouits N, Malliavin TE, Guizani I, Nilges M, Blondel A, Bouvier G.

BMC Bioinformatics. 2015 Mar 21;16:93. doi: 10.1186/s12859-015-0518-z.

18.

Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA.

Mareuil F, Malliavin TE, Nilges M, Bardiaux B.

J Biomol NMR. 2015 Aug;62(4):425-38. doi: 10.1007/s10858-015-9928-5. Epub 2015 Apr 11.

19.

Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling.

Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE.

J Cheminform. 2015 Jan 16;7:1. doi: 10.1186/s13321-014-0049-z. eCollection 2015.

20.

An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

Cassioli A, Bardiaux B, Bouvier G, Mucherino A, Alves R, Liberti L, Nilges M, Lavor C, Malliavin TE.

BMC Bioinformatics. 2015 Jan 28;16:23. doi: 10.1186/s12859-015-0451-1.

21.

Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts.

Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A.

Future Med Chem. 2014;6(18):2029-56. doi: 10.4155/fmc.14.137.

22.

Allosteric activation of Bordetella pertussis adenylyl cyclase by calmodulin: molecular dynamics and mutagenesis studies.

Selwa E, Davi M, Chenal A, Sotomayor-Pérez AC, Ladant D, Malliavin TE.

J Biol Chem. 2014 Jul 25;289(30):21131-41.

23.

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

Selwa E, Huynh T, Ciccotti G, Maragliano L, Malliavin TE.

Proteins. 2014 Oct;82(10):2483-96. doi: 10.1002/prot.24612. Epub 2014 Jun 9.

24.

Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

Mohammad Hosseini Naveh Z, Malliavin TE, Maragliano L, Cottone G, Ciccotti G.

PLoS One. 2014 Feb 13;9(2):e88555. doi: 10.1371/journal.pone.0088555. eCollection 2014.

25.

Functional motions modulating VanA ligand binding unraveled by self-organizing maps.

Bouvier G, Duclert-Savatier N, Desdouits N, Meziane-Cherif D, Blondel A, Courvalin P, Nilges M, Malliavin TE.

J Chem Inf Model. 2014 Jan 27;54(1):289-301. doi: 10.1021/ci400354b. Epub 2014 Jan 15.

PMID:
24397493
26.

Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors.

Miri L, Bouvier G, Kettani A, Mikou A, Wakrim L, Nilges M, Malliavin TE.

Proteins. 2014 Mar;82(3):466-78. doi: 10.1002/prot.24412. Epub 2013 Oct 17.

PMID:
24038133
27.

Blind testing of routine, fully automated determination of protein structures from NMR data.

Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.

Structure. 2012 Feb 8;20(2):227-36. doi: 10.1016/j.str.2012.01.002.

28.

Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis.

Selwa E, Laine E, Malliavin TE.

Proteins. 2012 Apr;80(4):1028-40. doi: 10.1002/prot.24005. Epub 2012 Jan 9.

PMID:
22231172
29.

The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations.

Duclert-Savatier N, Martínez L, Nilges M, Malliavin TE.

BMC Struct Biol. 2011 Nov 24;11:46. doi: 10.1186/1472-6807-11-46.

30.

Grid computing for improving conformational sampling in NMR structure calculation.

Mareuil F, Blanchet C, Malliavin TE, Nilges M.

Bioinformatics. 2011 Jun 15;27(12):1713-4. doi: 10.1093/bioinformatics/btr255. Epub 2011 May 5.

PMID:
21546391
31.

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

Martínez L, Malliavin TE, Blondel A.

Proteins. 2011 May;79(5):1649-61. doi: 10.1002/prot.22991. Epub 2011 Mar 21.

PMID:
21425348
32.

Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures.

Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE.

Proteins. 2011 May;79(5):1525-37. doi: 10.1002/prot.22980. Epub 2011 Mar 1.

PMID:
21365680
33.

Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding.

Laine E, Martínez L, Blondel A, Malliavin TE.

Biophys J. 2010 Oct 6;99(7):2264-72. doi: 10.1016/j.bpj.2010.07.044.

34.

Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor.

Laine E, Goncalves C, Karst JC, Lesnard A, Rault S, Tang WJ, Malliavin TE, Ladant D, Blondel A.

Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11277-82. doi: 10.1073/pnas.0914611107. Epub 2010 Jun 7.

35.

Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization.

Bardiaux B, Favier A, Etzkorn M, Baldus M, Böckmann A, Nilges M, Malliavin TE.

Adv Appl Bioinform Chem. 2010;3:25-38. Epub 2010 Jun 9.

36.

CASD-NMR: critical assessment of automated structure determination by NMR.

Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM.

Nat Methods. 2009 Sep;6(9):625-6. doi: 10.1038/nmeth0909-625. No abstract available.

37.

ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis.

Martínez L, Laine E, Malliavin TE, Nilges M, Blondel A.

Proteins. 2009 Dec;77(4):971-83. doi: 10.1002/prot.22523.

PMID:
19705488
38.

Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex.

Laine E, Blondel A, Malliavin TE.

Biophys J. 2009 Feb 18;96(4):1249-63. doi: 10.1016/j.bpj.2008.10.055. Erratum in: Biophys J. 2010 Jan 6;98(1):174.

39.

Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA.

Bardiaux B, Bernard A, Rieping W, Habeck M, Malliavin TE, Nilges M.

Proteins. 2009 May 15;75(3):569-85. doi: 10.1002/prot.22268.

PMID:
18951392
40.

Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA.

Bardiaux B, Bernard A, Rieping W, Habeck M, Malliavin TE, Nilges M.

BMC Struct Biol. 2008 Jun 5;8:30. doi: 10.1186/1472-6807-8-30.

41.

The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis.

Laine E, Yoneda JD, Blondel A, Malliavin TE.

Proteins. 2008 Jun;71(4):1813-29. doi: 10.1002/prot.21862.

PMID:
18175311
42.

A general algorithm for peak-tracking in multi-dimensional NMR experiments.

Ravel P, Kister G, Malliavin TE, Delsuc MA.

J Biomol NMR. 2007 Apr;37(4):265-75. Epub 2007 Feb 10.

PMID:
17294057
43.
44.

ARIA2: automated NOE assignment and data integration in NMR structure calculation.

Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M.

Bioinformatics. 2007 Feb 1;23(3):381-2. Epub 2006 Nov 22.

PMID:
17121777
45.

Comparison of different torsion angle approaches for NMR structure determination.

Bardiaux B, Malliavin TE, Nilges M, Mazur AK.

J Biomol NMR. 2006 Mar;34(3):153-66.

PMID:
16604424
46.

From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei.

Marin A, Malliavin TE, Nicolas P, Delsuc MA.

J Biomol NMR. 2004 Sep;30(1):47-60.

PMID:
15452434
47.

NMRb: a web-site repository for raw NMR datasets.

Pons JL, Malliavin TE, Tramesel D, Delsuc MA.

Bioinformatics. 2004 Dec 12;20(18):3707-9. Epub 2004 Jul 29.

PMID:
15284093
48.

Molecular dynamics simulations of HPr under hydrostatic pressure.

Canalia M, Malliavin TE, Kremer W, Kalbitzer HR.

Biopolymers. 2004 Aug 5;74(5):377-88. Erratum in: Biopolymers. 2004 Aug 15;74(6):495.

PMID:
15222017
49.

Stability of the I-motif structure is related to the interactions between phosphodiester backbones.

Malliavin TE, Gau J, Snoussi K, Leroy JL.

Biophys J. 2003 Jun;84(6):3838-47.

50.

Analysis of peptide rotational diffusion by homonuclear NMR.

Malliavin TE, Giudice E.

Biopolymers. 2002 Apr 15;63(5):335-42.

PMID:
11877743

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