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Items: 1 to 50 of 237

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

PMID:
28966015
6.

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.

7.

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.

8.

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.

9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

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
15.

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
16.

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
17.

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
18.

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
19.

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.

20.

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
21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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
30.

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.

31.

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.

32.

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
33.

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.

34.

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.

35.

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
36.

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
37.

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.

38.

Convective Replica-Exchange in Ergodic Regimes.

Signorini GF, Giovannelli E, Spill YG, Nilges M, Chelli R.

J Chem Theory Comput. 2014 Mar 11;10(3):953-8. doi: 10.1021/ct401033g.

PMID:
26580174
39.

Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase.

Chakraborty S, Reed J, Ross M, Nilges MJ, Petrik ID, Ghosh S, Hammes-Schiffer S, Sage JT, Zhang Y, Schulz CE, Lu Y.

Angew Chem Int Ed Engl. 2014 Feb 24;53(9):2417-21. doi: 10.1002/anie.201308431. Epub 2014 Jan 31.

40.

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
41.

Copper-sulfenate complex from oxidation of a cavity mutant of Pseudomonas aeruginosa azurin.

Sieracki NA, Tian S, Hadt RG, Zhang JL, Woertink JS, Nilges MJ, Sun F, Solomon EI, Lu Y.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):924-9. doi: 10.1073/pnas.1316483111. Epub 2014 Jan 3.

42.

Direct EPR observation of a tyrosyl radical in a functional oxidase model in myoglobin during both H2O2 and O2 reactions.

Yu Y, Mukherjee A, Nilges MJ, Hosseinzadeh P, Miner KD, Lu Y.

J Am Chem Soc. 2014 Jan 29;136(4):1174-1177. doi: 10.1021/ja4091885. Epub 2014 Jan 14.

43.

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes.

Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M.

J Synchrotron Radiat. 2014 Jan;21(Pt 1):203-8. doi: 10.1107/S1600577513030117. Epub 2013 Dec 14.

44.

ModBase, a database of annotated comparative protein structure models and associated resources.

Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D336-46. doi: 10.1093/nar/gkt1144. Epub 2013 Nov 23.

45.

Activation of the G-protein coupled receptor 30 (GPR30) has different effects on anxiety in male and female mice.

Hart D, Nilges M, Pollard K, Lynn T, Patsos O, Shiel C, Clark SM, Vasudevan N.

Steroids. 2014 Mar;81:49-56. doi: 10.1016/j.steroids.2013.11.004. Epub 2013 Nov 14.

PMID:
24240011
46.

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
47.

Recommendations of the wwPDB NMR Validation Task Force.

Montelione GT, Nilges M, Bax A, Güntert P, Herrmann T, Richardson JS, Schwieters CD, Vranken WF, Vuister GW, Wishart DS, Berman HM, Kleywegt GJ, Markley JL.

Structure. 2013 Sep 3;21(9):1563-70. doi: 10.1016/j.str.2013.07.021.

48.

In Silico screening on the three-dimensional model of the Plasmodium vivax SUB1 protease leads to the validation of a novel anti-parasite compound.

Bouillon A, Giganti D, Benedet C, Gorgette O, Pêtres S, Crublet E, Girard-Blanc C, Witkowski B, Ménard D, Nilges M, Mercereau-Puijalon O, Stoven V, Barale JC.

J Biol Chem. 2013 Jun 21;288(25):18561-73. doi: 10.1074/jbc.M113.456764. Epub 2013 May 7.

49.

Isolation of a mixed valence diiron hydride: evidence for a spectator hydride in hydrogen evolution catalysis.

Wang W, Nilges MJ, Rauchfuss TB, Stein M.

J Am Chem Soc. 2013 Mar 6;135(9):3633-9. doi: 10.1021/ja312458f. Epub 2013 Feb 21.

PMID:
23383865
50.

A convective replica-exchange method for sampling new energy basins.

Spill YG, Bouvier G, Nilges M.

J Comput Chem. 2013 Jan 15;34(2):132-40. doi: 10.1002/jcc.23113. Epub 2012 Sep 7. Erratum in: J Comput Chem. 2013 Jul 5;34(18):1609.

PMID:
22961200

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