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Items: 1 to 20 of 47

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.

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.

7.

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.

8.

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
9.

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.

10.

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
11.

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.

12.

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.

13.

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.

14.

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
15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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