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Items: 1 to 50 of 250

1.

Opioid-enhancing antinociceptive effects of delta-9-tetrahydrocannabinol and amitriptyline in rhesus macaques.

Nilges MR, Bondy ZB, Grace JA, Winsauer PJ.

Exp Clin Psychopharmacol. 2019 Aug 29. doi: 10.1037/pha0000313. [Epub ahead of print]

PMID:
31464475
2.

mkgridXf: Consistent Identification of Plausible Binding Sites Despite the Elusive Nature of Cavities and Grooves in Protein Dynamics.

Monet D, Desdouits N, Nilges M, Blondel A.

J Chem Inf Model. 2019 Aug 26;59(8):3506-3518. doi: 10.1021/acs.jcim.9b00103. Epub 2019 Jul 25.

PMID:
31287306
3.

Discriminative Stimulus and Low Abuse Liability Effects of Novel Endomorphin Analogs Suggest a Potential Treatment Indication for Opioid Use Disorder.

Nilges MR, Laurent M, Cable C, Arens L, Vafiades J, Zadina JE.

J Pharmacol Exp Ther. 2019 Sep;370(3):369-379. doi: 10.1124/jpet.118.253013. Epub 2019 Jun 18.

4.

Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches.

Bardiaux B, Cordier F, Brier S, López-Castilla A, Izadi-Pruneyre N, Nilges M.

J Biomol NMR. 2019 Jul;73(6-7):293-303. doi: 10.1007/s10858-019-00246-4. Epub 2019 May 23.

5.

Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus.

Bardiaux B, de Amorim GC, Luna Rico A, Zheng W, Guilvout I, Jollivet C, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O.

Structure. 2019 Jul 2;27(7):1082-1093.e5. doi: 10.1016/j.str.2019.03.021. Epub 2019 May 2.

PMID:
31056419
6.

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.

7.

Target Engagement and Binding Mode of an Antituberculosis Drug to Its Bacterial Target Deciphered in Whole Living Cells by NMR.

Bouvier G, Simenel C, Jang J, Kalia NP, Choi I, Nilges M, Pethe K, Izadi-Pruneyre N.

Biochemistry. 2019 Feb 12;58(6):526-533. doi: 10.1021/acs.biochem.8b00975. Epub 2019 Jan 3.

PMID:
30521325
8.

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.

9.

Effects of cocaine on the discriminative stimulus and reinforcing effects of mephedrone in male rats.

Erwin LL, Nilges MR, Bondy ZB, Winsauer PJ.

Psychopharmacology (Berl). 2019 Mar;236(3):1043-1056. doi: 10.1007/s00213-018-5110-6. Epub 2018 Nov 17.

PMID:
30448991
10.

Effects of noncontingent ethanol, DHEA, and pregnanolone administration on ethanol self-administration in outbred female rats.

Erwin LL, Nilges MR, DeLarge AF, Weed PF, Winsauer PJ.

Alcohol. 2019 Mar;75:67-77. doi: 10.1016/j.alcohol.2018.05.003. Epub 2018 May 9.

PMID:
30445249
11.

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R.

Structure. 2019 Jan 2;27(1):175-188.e6. doi: 10.1016/j.str.2018.09.011. Epub 2018 Nov 1.

PMID:
30393052
12.

A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme.

Mirts EN, Petrik ID, Hosseinzadeh P, Nilges MJ, Lu Y.

Science. 2018 Sep 14;361(6407):1098-1101. doi: 10.1126/science.aat8474.

13.

Near-Infrared Photoactivatable Nitric Oxide Donors with Integrated Photoacoustic Monitoring.

Zhou EY, Knox HJ, Reinhardt CJ, Partipilo G, Nilges MJ, Chan J.

J Am Chem Soc. 2018 Sep 19;140(37):11686-11697. doi: 10.1021/jacs.8b05514. Epub 2018 Sep 10.

PMID:
30198716
14.

Ordering Protein Contact Matrices.

Xu C, Bouvier G, Bardiaux B, Nilges M, Malliavin T, Lisser A.

Comput Struct Biotechnol J. 2018 Mar 16;16:140-156. doi: 10.1016/j.csbj.2018.03.001. eCollection 2018.

15.

Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase.

Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E.

Nucleic Acids Res. 2018 Mar 16;46(5):2660-2677. doi: 10.1093/nar/gky044.

16.

Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A.

Harigua-Souiai E, Abdelkrim YZ, Bassoumi-Jamoussi I, Zakraoui O, Bouvier G, Essafi-Benkhadir K, Banroques J, Desdouits N, Munier-Lehmann H, Barhoumi M, Tanner NK, Nilges M, Blondel A, Guizani I.

PLoS Negl Trop Dis. 2018 Jan 18;12(1):e0006160. doi: 10.1371/journal.pntd.0006160. eCollection 2018 Jan.

17.

Structure of the calcium-dependent type 2 secretion pseudopilus.

López-Castilla A, Thomassin JL, Bardiaux B, Zheng W, Nivaskumar M, Yu X, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O.

Nat Microbiol. 2017 Dec;2(12):1686-1695. doi: 10.1038/s41564-017-0041-2. Epub 2017 Oct 9.

18.

Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem.

Delhommel F, Cordier F, Bardiaux B, Bouvier G, Colcombet-Cazenave B, Brier S, Raynal B, Nouaille S, Bahloul A, Chamot-Rooke J, Nilges M, Petit C, Wolff N.

Structure. 2017 Nov 7;25(11):1645-1656.e5. doi: 10.1016/j.str.2017.08.013. Epub 2017 Sep 28.

19.

SAS profile correlations reveal SAS hierarchical nature and information content.

Spill YG, Nilges M.

PLoS One. 2017 May 11;12(5):e0177309. doi: 10.1371/journal.pone.0177309. eCollection 2017.

20.

Nicotine reverses hypofrontality in animal models of addiction and schizophrenia.

Koukouli F, Rooy M, Tziotis D, Sailor KA, O'Neill HC, Levenga J, Witte M, Nilges M, Changeux JP, Hoeffer CA, Stitzel JA, Gutkin BS, DiGregorio DA, Maskos U.

Nat Med. 2017 Mar;23(3):347-354. doi: 10.1038/nm.4274. Epub 2017 Jan 23.

21.

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data.

Carstens S, Nilges M, Habeck M.

PLoS Comput Biol. 2016 Dec 27;12(12):e1005292. doi: 10.1371/journal.pcbi.1005292. eCollection 2016 Dec.

22.

In Silico prediction of the molecular basis of ClTx and AaCTx interaction with matrix metalloproteinase-2 (MMP-2) to inhibit glioma cell invasion.

Othman H, Wieninger SA, ElAyeb M, Nilges M, Srairi-Abid N.

J Biomol Struct Dyn. 2017 Oct;35(13):2815-2829. doi: 10.1080/07391102.2016.1231633. Epub 2016 Sep 28.

PMID:
27678152
23.

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.

24.

Mechanism of H2 Production by Models for the [NiFe]-Hydrogenases: Role of Reduced Hydrides.

Ulloa OA, Huynh MT, Richers CP, Bertke JA, Nilges MJ, Hammes-Schiffer S, Rauchfuss TB.

J Am Chem Soc. 2016 Jul 27;138(29):9234-45. doi: 10.1021/jacs.6b04579. Epub 2016 Jul 18.

25.

Reversible S-nitrosylation in an engineered azurin.

Tian S, Liu J, Cowley RE, Hosseinzadeh P, Marshall NM, Yu Y, Robinson H, Nilges MJ, Blackburn NJ, Solomon EI, Lu Y.

Nat Chem. 2016 Jul;8(7):670-7. doi: 10.1038/nchem.2489. Epub 2016 Apr 25.

26.

Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling.

Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J.

Mol Cell Proteomics. 2016 Aug;15(8):2730-43. doi: 10.1074/mcp.M115.056473. Epub 2016 Jun 1.

27.

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
28.

A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site.

Hosseinzadeh P, Tian S, Marshall NM, Hemp J, Mullen T, Nilges MJ, Gao YG, Robinson H, Stahl DA, Gennis RB, Lu Y.

J Am Chem Soc. 2016 May 25;138(20):6324-7. doi: 10.1021/jacs.5b13128. Epub 2016 May 12.

PMID:
27120678
29.

Automated structure modeling of large protein assemblies using crosslinks as distance restraints.

Ferber M, Kosinski J, Ori A, Rashid UJ, Moreno-Morcillo M, Simon B, Bouvier G, Batista PR, Müller CW, Beck M, Nilges M.

Nat Methods. 2016 Jun;13(6):515-20. doi: 10.1038/nmeth.3838. Epub 2016 Apr 25.

PMID:
27111507
30.

Monoanionic bis(carbene) pincer complexes featuring cobalt(I-III) oxidation states.

Ibrahim AD, Tokmic K, Brennan MR, Kim D, Matson EM, Nilges MJ, Bertke JA, Fout AR.

Dalton Trans. 2016 Jun 14;45(24):9805-11. doi: 10.1039/c5dt04723d.

PMID:
26778113
31.

Endomorphin analog analgesics with reduced abuse liability, respiratory depression, motor impairment, tolerance, and glial activation relative to morphine.

Zadina JE, Nilges MR, Morgenweck J, Zhang X, Hackler L, Fasold MB.

Neuropharmacology. 2016 Jun;105:215-227. doi: 10.1016/j.neuropharm.2015.12.024. Epub 2015 Dec 31.

PMID:
26748051
32.

Design of a single protein that spans the entire 2-V range of physiological redox potentials.

Hosseinzadeh P, Marshall NM, Chacón KN, Yu Y, Nilges MJ, New SY, Tashkov SA, Blackburn NJ, Lu Y.

Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):262-7. doi: 10.1073/pnas.1515897112. Epub 2015 Dec 2.

33.

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
34.

Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation.

Gault J, Ferber M, Machata S, Imhaus AF, Malosse C, Charles-Orszag A, Millien C, Bouvier G, Bardiaux B, Péhau-Arnaudet G, Klinge K, Podglajen I, Ploy MC, Seifert HS, Nilges M, Chamot-Rooke J, Duménil G.

PLoS Pathog. 2015 Sep 14;11(9):e1005162. doi: 10.1371/journal.ppat.1005162. eCollection 2015 Sep.

35.

Binuclear Cu(A) Formation in Biosynthetic Models of Cu(A) in Azurin Proceeds via a Novel Cu(Cys)2His Mononuclear Copper Intermediate.

Chakraborty S, Polen MJ, Chacón KN, Wilson TD, Yu Y, Reed J, Nilges MJ, Blackburn NJ, Lu Y.

Biochemistry. 2015 Oct 6;54(39):6071-81. doi: 10.1021/acs.biochem.5b00659.

36.

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.

37.

ESR and X-ray Structure Investigations on the Binding and Mechanism of Inhibition of the Native State of Myeloperoxidase with Low Molecular Weight Fragments.

Chavali B, Masquelin T, Nilges MJ, Timm DE, Stout SL, Matter WF, Jin N, Jadhav PK, Deng GG.

Appl Magn Reson. 2015;46(8):853-873. Epub 2015 May 19.

38.

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.

Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD.

Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18.

39.

NMR Exchange Format: a unified and open standard for representation of NMR restraint data.

Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW.

Nat Struct Mol Biol. 2015 Jun;22(6):433-4. doi: 10.1038/nsmb.3041. No abstract available.

40.

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.

41.

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.

42.

Exploring Mn-O bonding in the context of an electronically flexible secondary coordination sphere: synthesis of a Mn(III)-oxo.

Park YJ, Matson EM, Nilges MJ, Fout AR.

Chem Commun (Camb). 2015 Mar 28;51(25):5310-3. doi: 10.1039/c4cc08603a.

PMID:
25745671
43.

Defining the role of tyrosine and rational tuning of oxidase activity by genetic incorporation of unnatural tyrosine analogs.

Yu Y, Lv X, Li J, Zhou Q, Cui C, Hosseinzadeh P, Mukherjee A, Nilges MJ, Wang J, Lu Y.

J Am Chem Soc. 2015 Apr 15;137(14):4594-7. doi: 10.1021/ja5109936. Epub 2015 Apr 1.

44.

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.

45.

An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps.

Bouvier G, Desdouits N, Ferber M, Blondel A, Nilges M.

Bioinformatics. 2015 May 1;31(9):1490-2. doi: 10.1093/bioinformatics/btu849. Epub 2014 Dec 26.

PMID:
25543048
46.

Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

Desdouits N, Nilges M, Blondel A.

J Mol Graph Model. 2015 Feb;55:13-24. doi: 10.1016/j.jmgm.2014.10.011. Epub 2014 Oct 25.

47.

Computational design of protein-based inhibitors of Plasmodium vivax subtilisin-like 1 protease.

Bastianelli G, Bouillon A, Nguyen C, Le-Nguyen D, Nilges M, Barale JC.

PLoS One. 2014 Oct 24;9(10):e109269. doi: 10.1371/journal.pone.0109269. eCollection 2014.

48.

Meridional vs. facial coordination geometries of a dipodal ligand framework featuring a secondary coordination sphere.

Matson EM, Gordon Z, Lin B, Nilges MJ, Fout AR.

Dalton Trans. 2014 Dec 7;43(45):16992-5. doi: 10.1039/c4dt02327g.

PMID:
25325404
49.

Redesigning the blue copper azurin into a redox-active mononuclear nonheme iron protein: preparation and study of Fe(II)-M121E azurin.

Liu J, Meier KK, Tian S, Zhang JL, Guo H, Schulz CE, Robinson H, Nilges MJ, Münck E, Lu Y.

J Am Chem Soc. 2014 Sep 3;136(35):12337-44. doi: 10.1021/ja505410u. Epub 2014 Aug 22.

PMID:
25082811
50.

Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers.

Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O.

Structure. 2014 May 6;22(5):685-96. doi: 10.1016/j.str.2014.03.001. Epub 2014 Mar 27.

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