A worldwide e-Infrastructure for NMR and structural biology

Publications acknowledging WeNMR

111 Webert H, Freibert SA, Gallo A, Heidenreich T, Linne U, Amlacher S, Hurt E, Mühlenhoff U, Banci L, Lill R. Functional reconstitution of mitochondrial Fe/S cluster synthesis on Isu1 reveals the involvement of ferredoxin.Nat Commun. 2014 5:5013. 10.1038/ncomms6013

110 Parigi G, Rezaei-Ghaleh N, Giachetti A, Becker S, Fernandez C, Blackledge M, Griesinger C, Zweckstetter M, Luchinat C. Long-Range Correlated Dynamics in Intrinsically Disordered Proteins. J Am Chem Soc. 2014 136:16201-9. 10.1021/ja506820r

109 Finci LI, Krüger N, Sun X, Zhang J, Chegkazi M, Wu Y, Schenk G, Mertens HD, Svergun DI, Zhang Y, Wang JH, Meijers R. The crystal structure of netrin-1 in complex with DCC reveals the bifunctionality of netrin-1 as a guidance cue. Neuron. 2014 83:839-49. 10.1016/j.neuron.2014.07.010

108 Banci L, Brancaccio D, Ciofi-Baffoni S, Del Conte R, Gadepalli R, Mikolajczyk M, Neri S, Piccioli M, Winkelmann J. [2Fe-2S] cluster transfer in iron-sulfur protein biogenesis. Proc Natl Acad Sci U S A. 2014 111:6203-8. 10.1073/pnas.140010211

107 Penumutchua SR, Choub R-H,Yu C. Interaction between S100P and the anti-allergy drug cromolyn. Biochem Biophy Res Comm 2014 454:404-9. 10.1016/j.bbrc.2014.10.048

106 Saponaro A, Pauleta SR, Cantini F, Matzapetakis M, Hammann C, Donadoni C, Hu L, Thiel G, Banci L, Santoro B, Moroni A. Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function. Proc Natl Acad Sci U S A. 2014 111:14577-82.  10.1073/pnas.1410389111

105 Penumutchu SR, Chou RH, Yu C. Structural insights into calcium-bound S100P and the V domain of the RAGE complex. PLoS One. 2014 9:e103947. 10.1371/journal.pone.0103947

104 Pavšič M, Gunčar G, Djinović-Carugo K, Lenarčič B. Crystal structure and its bearing towards an understanding of key biological functions of EpCAM. Nat Commun. 2014 5:4764. 10.1038/ncomms5764.

103 Gorbatyuk V, Nguyen K, Podolnikova NP, Deshmukh L, Lin X, Ugarova TP, Vinogradova O. Skelemin Association with αIIbβ3 Integrin: A Structural Model. Biochemistry. 2014 53:6766-75. 10.1021/bi500680s

102 Zhang Z, Porter J, Tripsianes K, Lange OF. Robust and highly accurate automatic NOESY assignment and structure determination with Rosetta. J Biomol NMR. 2014 59:135-45. 10.1007/s10858-014-9832-4

101 Cerofolini L, Amato J, Giachetti A, Limongelli V, Novellino E, Parrinello M, Fragai M, Randazzo A, Luchinat C G-triplex structure and formation propensity. Nucleic Acids Res. 2014 In press 10.1093/nar/gku1084

100 Cacciatore S, Luchinat C, Tenori L. Knowledge discovery by accuracy maximization. Proc Natl Acad Sci U S A. 2014 111:5117-22. 10.1073/pnas.1220873111

99 Helmling C, Bessi I, Wacker A, Schnorr KA, Jonker HR, Richter C, Wagner D, Kreibich M, Schwalbe H. Non-covalent spin labeling of riboswitch RNAs to obtain long-range structural NMR restraints. ACS Chem Biol. 2014 9:1330-9. 10.1021/cb500050t

98 Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RK, Turner DH1 Das R. Structure determination of noncanonical RNA motifs guided by (1)H NMR chemical shifts. Nat Methods. 2014, 11:413-6. 10.1038/nmeth.2876

97 Wu WJ, Su MI, Wu JL, Kumar S, Lim LH, Wang CW, Nelissen FH, Chen MC, Doreleijers JF, Wijmenga SS, Tsai MD. How a low-fidelity DNA polymerase chooses non-watson-crick from watson-crick incorporation. J Am Chem Soc. 2014, 136:4927-37 10.1021/ja4102375

96 Stark JL, Mehla K, Chaika N, Acton TB, Xiao R, Singh PK, Montelione GT, Powers R. Structure and Function of Human DnaJ Homologue Subfamily A Member 1 (DNAJA1) and Its Relationship to Pancreatic Cancer.Biochemistry. 2014, 53:1360-72. 10.1021/bi401329a

95 van Zundert GCP, Bonvin AMJJ. Modeling Protein–Protein Complexes Using the HADDOCK Webserver. Protein Structure Prediction - Methods in Molecular Biology 2014 1137:163-179

94 van Breugel M, Wilcken R, McLaughlin SH, Rutherford TJ, Johnson CM Structure of the SAS-6 cartwheel hub from Leishmania major eLife 2014:e01812 10.7554/eLife.01812

93 Steinert HS,Florian Schäfer F,Jonker HRA, Heckel A, Schwalbe H. Influence of the Absolute Configuration of NPE-Caged Cytosine on DNA Single Base Pair Stability Angewandte Chemie 2014 126:1090–1093 10.1002/ange.201307852

92 Bhaumik A, Luchinat C, Parigi G, Ravera E, Rinaldelli M. NMR crystallography on paramagnetic systems: solved and open issues. CrystEngComm 2013 15:8639-8656 10.1039/C3CE41485J

91 Shumilina E, Dobrovolska O, Del Conte R, Holen HW, Dikiy A. Competitive cobalt for zinc substitution in mammalian methionine sulfoxide reductase B1 overexpressed in E. coli: structural and functional insight. J Biol Inorg Chem. 2014 19:85-95 10.1007/s00775-013-1064-7

90 Leyrat C, Renner M, Harlos K, Grimes JM. Solution and crystallographic structures of the central region of the phosphoprotein from human metapneumovirus. PLoS One. 2013 8:e80371. 10.1371/journal.pone.0080371

89 Varney KM, Bonvin AM, Pazgier M, Malin J, Yu W, Ateh E, Oashi T, Lu W, Huang J, Diepeveen-de Buin M, Bryant J, Breukink E, Mackerell AD Jr, de Leeuw EP. Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II. PLoS Pathog. 2013 9:e1003732. 10.1371/journal.ppat.1003732

88 Vuister GW, Fogh RH, Hendrickx PM, Doreleijers JF, Gutmanas A. An overview of tools for the validation of protein NMR structures. J Biomol NMR. 2013 In press 10.1007/s10858-013-9750-x

87 Karaca E, Bonvin AMJJ. On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. Acta Cryst. 2013 D69:683-694  10.1107/S0907444913007063

86 Sander B, Tria G, Shkumatov AV, Kim E.-Y., Grossmann JG, Tessmer I,  Svergun DI, Schindelin H. Structural characterization of gephyrin by AFM and SAXS reveals a mixture of compact and extended states. Acta Cryst. 2013 D69:2050-2060  10.1107/S0907444913018714 

85 Söderberg CA, Rajan S, Shkumatov AV, Gakh O, Schaefer S, Ahlgren EC, Svergun DI, Isaya G, Al-Karadaghi S. The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization. J Biol Chem. 2013 288(12):8156-67. 10.1074/jbc.M112.442285

84 Kovalevskaya NV, van de Waterbeemd M, Bokhovchuk FM, Bate N, Bindels RJ, Hoenderop JG, Vuister GW. Structural analysis of calmodulin binding to ion channels demonstrates the role of its plasticity in regulation Pflugers Arch Eur J Physiol. 2013 465:1507-1519 10.1007/s00424-013-1278-0

83 Dölker N, Blanchet CE, Voß B, Haselbach D, Kappel C, Monecke T, Svergun DI, Stark H, Ficner R, Zachariae U, Grubmüller H, Dickmanns A. Structural determinants and mechanism of mammalian CRM1 allostery. Structure. 2013 21:1350-60 10.1016/j.str.2013.05.015

82 Banci L, Bertini I, Calderone V, Ciofi-Baffoni S, Giachetti A, Jaiswal D, Mikolajczyk M, Piccioli M, Winkelmann J. Molecular view of an electron transfer process essential for iron-sulfur protein biogenesis. Proc Natl Acad Sci U S A. 2013 110:7136-41 10.1073/pnas.1302378110

81 Gupta AA, Chou RH, Li H, Yang LW, Yu C. Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling. Biochim Biophys Acta. 2013 1834:2606-2619. 10.1016/j.bbapap.2013.09.012

80 Rosato A, Tejero R, Montelione GT. Quality assessment of protein NMR structures Current Op Struct Biol 2013 23:715–724 10.1016/j.sbi.2013.08.005

79 Nowak E, Potrzebowski W, Konarev PV, Rausch JW, Bona MK, Svergun DI, Bujnicki JM, Le Grice SF, Nowotny M. Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid. Nucleic Acids Res. 2013 41:3874-87. 10.1093/nar/gkt053.

78 Cerofolini L, Fields GB, Fragai M, Geraldes CF, Luchinat C, Parigi G, Ravera E, Svergun DI, Teixeira JM. Examination of matrix metalloproteinase-1 (MMP-1) in solution: a preference for the pre-collagenolysis state. J Biol Chem. 2013  288:30659-30671.10.1074/jbc.M113.477240

77 Viegas A, Sardinha J, Freire F, Duarte DF, Carvalho AL, Fontes CM, Romão MJ, Macedo AL, Cabrita EJ. Solution structure, dynamics and binding studies of a family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11). Biochem J. 2013 451:289-300. 10.1042/BJ20120627.

76 Silvers R, Schwalbe H. Detecting Intracellular Cysteine Redox States by in-Cell NMR Spectroscopy. Chembiochem. 2013 14:1705-7. 10.1002/cbic.201300379.

75 Nielsen G, Jonker HRA, Vajpai N, Grzesiek S,Schwalbe H. Kinase in Motion: Insights into the Dynamic Nature of p38α by High-Pressure NMR Spectroscopic Studies. 2013 14:1799-1806 10.1002/cbic.201300170

74  Sahoo N, Goradia N, Ohlenschläger O, Schönherr R, Friedrich M, Plass W, Kappl R, Hoshi T, Heinemann SH. Heme impairs the ball-and-chain inactivation of potassium channels. Proc Natl Acad Sci U S A. 2013 110:E4036-44. 10.1073/pnas.1313247110.

73 Rodrigues JP, Melquiond AS, Karaca E, Trellet M, van Dijk M, van Zundert GC, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AM. Defining the limits of homology modeling in information-driven protein docking. Proteins. 2013 81:2119-2128. 10.1002/prot.24382

72 Cukkemane A, Baldus M. Characterization of a cyclic nucleotide-activated K(+) channel and its lipid environment by using solid-state NMR spectroscopy. Chembiochem. 2013 14:1789-98. 10.1002/cbic.201300182.

71 Morris C. Towards a structural biology work bench. Acta Cryst. 2013 D69:681-682 10.1107/S090744491300276X.

70 van der Schot G, Zhang Z, Vernon R, Shen Y, Vranken WF, Baker D, Bonvin AM, Lange OF. Improving 3D structure prediction from chemical shift data. J Biomol NMR. 2013 57:27-35. 10.1007/s10858-013-9762-6.

69 Takacs M, Petoukhov MV, Atkinson RA, Roblin P, Ogi FX, Demeler B, Potier N, Chebaro Y, Dejaegere A, Svergun DI, Moras D, Billas IM. The asymmetric binding of PGC-1α to the ERRα and ERRγ nuclear receptor homodimers involves a similar recognition mechanism. PLoS One. 2013 8:e67810. 10.1371/journal.pone.0067810

68 Dagil R, O'Shea C, Nykjær A, Bonvin AM, Kragelund BB. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin. J Biol Chem. 2013 288:4424-35. 10.1074/jbc.M112.434159.

67 Aranko AS, Oeemig JS, Iwaï H. Structural basis for Protein Trans-Splicing by a Bacterial Intein-Like domain: Protein Ligation without Nucleophilic side-chains. FEBS J. 2013 14:3256–3269 10.1111/febs.12307.

66 Mehtälä ML, Haataja TJ, Blanchet CE, Hiltunen JK, Svergun DI, Glumoff T. Quaternary structure of human, Drosophila melanogaster and Caenorhabditis elegans MFE-2 in solution from synchrotron small-angle X-ray scattering. FEBS Lett. 2013 587:305-10. 10.1016/j.febslet.2012.12.014

65 Bertini I, Borsi V, Cerofolini L, Das Gupta S, Fragai M, Luchinat C. Solution structure and dynamics of human S100A14 J Biol Inorg Chem 2013 18:183-194 10.1007/s00775-012-0963-3

64 Wegerich, Giachetti A, Allegrozzi M, Lisdat F, Turano P. Mechanistic insights into the superoxide–cytochrome c reaction by lysine surface scanning J Biol Inorg Chem 2013 18: 429-440 10.1007/s00775-013-0987-3

63 Dijk M, Visscher, KM, Kastritis, PL, Bonvin AMJJ. Solvated protein-DNA docking using HADDOCK. J Biomol NMR. 2013 56:51-63 10.1007/s10858-013-9734-x

62 Trellet M, Melquiond ASJ, Bonvin AMJJ. A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking. PLoS ONE 2013 8:e58769. 10.1371/journal.pone.0058769
 
61Lamber EP, Beuron F, Morris EP, Svergun DI, Mittnacht S. Structural insights into the mechanism of phosphoregulation of the retinoblastoma protein PLOS One 2013, 8:e58463 10.1371/journal.pone.0058463

60 Manta B, Pavan C, Sturlese M, Medeiros A, Crispo M, Berndt C, Krauth-Siegel RL, Bellanda M, Comini MA. Iron-Sulfur Cluster Binding by Mitochondrial Monothiol Glutaredoxin-1 of Trypanosoma brucei: Molecular Basis of Iron-Sulfur Cluster Coordination and Relevance for Parasite Infectivity. Antioxid Redox Signal 2013 19:665-682 10.1089/ars.2012.4859

59 Rybka K, Toal SE, Verbaro DJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Disorder and order in unfolded and disordered peptides and proteins: A view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations. Proteins 2013 6:968–983 10.1002/prot.24226

58 Cilia E, Vuister GW, Lenaerts T. Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e. PLoS Comput Biol 2012, 8:e1002794. 10.1371/journal.pcbi.1002794

57 Karaca E, Bonvin AMJJ. Advances in integrative modeling of biomolecular complexes. Methods 2013 59:372-381 10.1016/j.ymeth.2012.12.004

56 Blanchet CE, Svergun DI. Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution Annual Review of Physical Chemistry 2013 64:37-54 10.1146/annurev-physchem-040412-110132

55 Wassenaar TA, van Dijk M, Loureiro-Ferreira N, van der Schot G, de Vries SJ, Schmitz C, van der Zwan J, Boelens R, Giachetti A, Ferella L, Rosato A, Bertini I, Herrmann T, Jonker HRA, Bagaria A, Jaravine V, Güntert P, Schwalbe H, Vranken WF,  Doreleijers JF, Vriend G, Vuister GW, Franke D, Kikhney A, Svergun DI, Fogh R, Ionides J, Laue ED, Spronk, C, Jurkša S, Verlato, M, Badoer S, Dal Pra S, Mazzucato M, Frizziero E, Bonvin AMJJ. WeNMR: Structural Biology on the Grid. J Grid Comp 2012, 10:743-767. 10.1007/s10723-012-9246-z

54 Stehle T, Sreeramulu S, Löhr F, Richter C, Saxena K, Jonker HR, Schwalbe H. The Apo-structure of the Low Molecular Weight Protein-tyrosine Phosphatase A (MptpA) from Mycobacterium tuberculosis Allows for Better Target-specific Drug Development. J Biol Chem. 2012 287:34569-34582. 10.1074/jbc.M112.399261

53 Nagulapalli M, Parigi G, Yuan J, Gsponer J, Deraos G, Bamm VV, Harauz G, Matsoukas J, de Planque MR, Gerothanassis IP, Babu MM, Luchinat C, Tzakos AG. Recognition pliability is coupled to structural heterogeneity: a calmodulin intrinsically disordered binding region complex. Structure. 2012 20:522-533. 10.1016/j.str.2012.01.021

52 Zoll S, Schlag M, Shkumatov AV, Rautenberg M, Svergun DI, Götz F, Stehle T. Ligand-binding properties and conformational dynamics of autolysin repeat domains in staphylococcal cell wall recognition. J Bacteriol. 2012 194:3789-3802. 10.1128/​JB.00331-12

51 Ribeiro Ede A Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K. Structural flexibility of RNA as molecular basis for Hfq chaperone function. Nucleic Acids Res. 2012 40:8072-84. 10.1093/nar/gks510

50 Elantak L, Espeli M, Boned A, Bornet O, Bonzi J, Gauthier L, Feracci M, Roche P, Guerlesquin F, Schiff C. Structural basis for galectin-1-dependent pre-B cell receptor (pre-BCR) activation. J Biol Chem. 2012 287: 44703-4471310.1074/jbc.M112.395152

49 Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW. CING: an integrated residue-based structure validation program suite. J Biomol NMR. 2012 54:267-283. 10.1007/s10858-012-9669-7

48 Gradmann S, Ader C, Heinrich I, Nand D, Dittmann M, Cukkemane A, van Dijk M, Bonvin AM, Engelhard M, Baldus M. Rapid prediction of multi-dimensional NMR data sets. J Biomol NMR. 2012 54:377-384. 10.1007/s10858-012-9681-y

47 Luchinat C, Nagulapalli M, Parigi G, Sgheri L. Maximum occurrence analysis of protein conformations for different distributions of paramagnetic metal ions within flexible two-domain proteins. J Magn Reson. 2012 215:85-93. 10.1016/j.jmr.2011.12.016

46 Bertini I, Luchinat C, Nagulapalli M, Parigi G, Ravera E. Paramagnetic relaxation enhancement for the characterization of the conformational heterogeneity in two-domain proteins. Phys Chem Chem Phys. 2012 14:9149-9156. 10.1039/C2CP40139H

45 Adrover M, Martorell G, Martin SR, Urosev D, Konarev PV, Svergun DI, Daura X, Temussi P, Pastore A. The role of hydration in protein stability: comparison of the cold and heat unfolded states of Yfh1. J Mol Biol. 2012 417:413-424. 10.1016/j.jmb.2012.02.002

44 Kastritis PL, van Dijk AD, Bonvin AM. Explicit treatment of water molecules in data-driven protein-protein docking: the solvated HADDOCKing approach. Methods Mol Biol. 2012 819:355-374. 10.1007/978-1-61779-465-0_22

43 Blanchet CE, Zozulya AV, Kikhney AG, Franke D, Konarev PV, Shang W, Klaering R, Robrahn B, Hermes C, Cipriani F, Svergun DI and Roessle M Instrumental setup for high-throughput small- and wide-angle solution scattering at the X33 beamline of EMBL Hamburg. J. Appl. Cryst. 2012 45:489-495 10.1107/S0021889812013490

42 Gallo A, Lo Sterzo C, Mori M, Di Matteo A, Bertini I, Banci L, Brunori M, Federici L. Structure of Nucleophosmin DNA-binding Domain and Analysis of Its Complex with a G-quadruplex Sequence from the c-MYC Promoter. J Biol Chem. 2012 287:26539-26548. 10.1074/jbc.M112.371013

41 Bernadó P, Svergun DI. Analysis of Intrinsically Disordered Proteins by Small-Angle X-ray Scattering. Methods Mol Biol. 2012 896:107-122. 10.1007/978-1-4614-3704-8_7

40 Banci L, Bertini I, Ciofi-Baffoni S, Jaiswal D, Neri S, Peruzzini R, Winkelmann J. Structural characterization of CHCHD5 and CHCHD7: Two atypical human twin CX(9)C proteins. J Struct Biol. 2012 180:190-200. 10.1016/j.jsb.2012.07.007

39 Wassenaar TA, de Vries S, Bonvin AMJJ, Bekker H. SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions. J. Chem. Theory Comput. 2012 8:3618-3627. 10.1021/ct3000662

38 Franke D, Kikhney AG, Svergun DI. Automated acquisition and analysis of small angle X-ray scattering data, Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 2012 689:52-59. 10.1016/j.nima.2012.06.008.

37 Gottstein D, Kirchner DK, Güntert P. Simultaneous single-structure and bundle representation of protein NMR structures in torsion angle space. J Biomol NMR. 2012 52:351-364. 10.1007/s10858-012-9615-8

36 Bertini I, Ferella L, Luchinat C, Parigi G, Petoukhov MV, Ravera E, Rosato A, Svergun DI. MaxOcc: a web portal for maximum occurrence analysis. J Biomol NMR. 2012 53:271-280. 10.1007/s10858-012-9638-1

35 Petoukhov MV, Franke D, Shkumatov AV, Tria G, Kikhney AG, Gajda M, Gorba C, Mertens HDT, Konarev PV, Svergun DI New developments in the ATSAS program package for small-angle scattering data analysis J. Appl. Cryst. 2012 45:342-350. 10.1107/S0021889812007662

34 Zou T, Yao X, Qin B, Zhang M, Cai L, Shang W, Svergun DI, Wang M, Cui S, Jin Q Crystal structure of Pseudomonas aeruginosa Tsi2 reveals a stably folded superhelical antitoxin J Mol Biol. 2012  417:351-361. 10.1016/j.jmb.2012.01.040

33 Oeemig JS,  Zhou D, Kajander T, Wlodawer A, Iwaï A NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein J Mol Biol 2012 421:85-99. 10.1016/j.jmb.2012.04.029

32 Luchinat C, Parigi C, Ravera E, Rinaldelli M Solid-State NMR Crystallography through Paramagnetic Restraints J Am Chem Soc. 2012 134:5006-5009. 10.1021/ja210079n

31 van Dijk M, Wassenaar TA, Bonvin AMJJ A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations J. Chem. Theory Comput. 2012 8:3463-3472. 10.1021/ct300102d

30 Huang YJ, Rosato A, Singh G, Montelione GT RPF: a quality assessment tool for protein NMR structures Nucleic Acids Research 2012 40(Web Server issue):W542-546. 10.1093/nar/gks373

29 Tomaselli S, Assfalg M, Pagano K, Cogliati C, Zanzoni S, Molinari H, Ragona L. A Disulfide Bridge Allows for Site-Selective Binding in Liver Bile Acid Binding Protein Thereby Stabilising the Orientation of Key Amino Acid Side Chains. Chemistry. 2012 18:2857-2866. 10.1002/chem.201102203

28 Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW. NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 2012 40(Database issue):D519-524. 10.1093/nar/gkr1134

27 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, de Vries S, Vuister GW, Wu B, Yang Y, Bonvin AM Blind testing of routine, fully automated determination of protein structures from NMR data. Structure. 2012 20:227-236. 10.1016/j.str.2012.01.002

26 Tottey S, Patterson CJ, Banci L, Bertini I, Felli IC, Pavelkova A, Dainty SJ, Pernil R, Waldron KJ, Foster AW, Robinson NJ. Cyanobacterial metallochaperone inhibits deleterious side reactions of copper. Proc Natl Acad Sci U S A. 2012 109:95-100. 10.1073/pnas.1117515109

25** Bagaria A, Jaravine V, Huang YJ, Montelione GT, Güntert P. Protein structure validation by generalized linear model root-mean-square deviation prediction; Protein Science 2012 21:229-238. 10.1002/pro.2007

24 Jimenez B, Ugwu F, Zhao R, Orti L, Makhnevych T, Pineda-Lucena A, Houry WA The structure of the minimal tetratricopeptide repeat domain protein Tah1 reveals the mechanism of its interaction with Pih1 and Hsp90 J Biol Chem. 2012 287:5698-5709 10.1074/jbc.M111.287458

23 Melquiond ASJ, Karaca E, Kastritis PL, Bonvin AMJJ Next challenges in protein-protein docking: From proteome to interactome and beyond WIREs Computational Molecular Science 2012 2:642-651. 10.1002/WCMS.91

22 Whelan F., Stead J., Shkumatov AV, Svergun DI, Sanders C, Antson AA A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding Nucleic Acids Research 2012 40:2271-2283 10.1093/nar/gkr906

21 Bertini I, Calderone V, Cerofolini L, Fragai M, Geraldes CF, Hermann P, Luchinat C, Parigi G, Teixeira JM The catalytic domain of MMP-1 studied through tagged lanthanides FEBS Lett 2012 586:557-567 10.1016/j.febslet.2011.09.020

20 Sgrignani J, Pierattelli R Nuclear magnetic resonance signal chemical shifts and molecular simulations: a multidisciplinary approach to modeling copper protein structures J Biol Inorg Chem. 2012 17:71-79. 10.1007/s00775-011-0830-7

19 Bernadó P, Svergun DI Structural analysis of intrinsically disordered proteins by small-angle X-ray scattering Mol Biosyst 2012 8:151-167 10.1039/C1MB05275F

18 Söderberg CA, Shkumatov AV, Rajan S, Gakh O, Svergun DI, Isaya G, Al-Karadaghi S.Oligomerization propensity and flexibility of yeast frataxin studied by X-ray crystallography and small-angle X-ray scattering. J Mol Biol. 2011 414:783-797. 10.1016/j.jmb.2011.10.034

17 Bertini I, Gonnelli L, Luchinat C, Mao J, Nesi A. A new structural model of Aβ40 fibrils. J Am Chem Soc. 2011 133:16013-16022. 10.1021/ja2035859

16* Dasgupta S, Hu X, Keizers PH, Liu WM, Luchinat C, Nagulapalli M, Overhand M, Parigi G, Sgheri L, Ubbink M Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains J Biomol NMR 2011 51:253-263 10.1007/s10858-011-9532-2

15 Banci L, Bertini I, Cefaro C, Ciofi-Baffoni S, Gallo A Functional role of two interhelical disulfide bonds in human cox17 protein from a structural perspective J Biol Chem 2011 286:34382-34390 10.1074/jbc.M111.246223

14 Banci L, Bertini I, Calderone V, Cefaro C, Ciofi-Baffoni S, Gallo A, Kallergi E, Lionaki E, Pozidis C, Tokatlidis K Molecular recognition and substrate mimicry drive the electron-transfer process between MIA40 and ALR Proc Natl Acad Sci USA 2011 108:4811-4816 10.1073/pnas.1014542108

13* Zanzoni S, Assfalg M, Giorgetti A, D'Onofrio M, Molinari H Structural requirements for cooperativity in ileal bile acid binding proteins J Biol Chem 2011 286:39307-39317 10.1074/jbc.M111.261099

12 Bertini I, Case DA, Ferella L, Giachetti A, Rosato A A Grid-enabled web portal for NMR structure refinement with AMBER Bioinformatics 2011 27:2384-2390 10.1093/bioinformatics/btr415

11 Bielnicki JA, Shkumatov AV, Derewenda U, Somlyo AV, Svergun DI, Derewenda ZS Insights into the Molecular Activation Mechanism of the RhoA-specific Guanine Nucleotide Exchange Factor, PDZRhoGEF J Biol Chem 2011 286:35163-35175 10.1074/jbc.M111.270918

10 Schmitz C, Bonvin AMJJ Protein-Protein HADDocking using exclusively Pseudocontact Shifts J Biomol NMR 2011 50:263-266 10.1007/s10858-011-9514-4

9 Stratmann D, Boelens R, Bonvin AMJJ Quantitative use of chemical shifts for the modelling of protein complexes Proteins 2011 79:2662-2670 10.1002/prot.23090

8 de Vries SJ, Bonvin AMJJ CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK PLoS One 2011 6(3):e17695 10.1371/journal.pone.0017695

7 Koehler C, Carlier L, Veggi D, Balducci E, Di Marcello F, Ferrer-Navarro M, Pizza M, Daura X, Soriani M, Boelens R, Bonvin AMJJ Structural and biochemical characterization of Nar E, an iron containing ADP-ribosyltransferase from Neisseria meningitides J Biol Chem 2011 286:14842-14851 10.1074/jbc.M110.193623

6 Karaca E, Bonvin AMJJ A multi-domain flexible docking approach to deal with large conformational changes in the modeling of biomolecular complexes Structure 2011 19:555-565 10.1016/j.str.2011.01.014

5 Krzeminski M, Singh T, André S, Lensch M, Wu AM, Bonvin AMJJ, Gabius HJ Human galectin-3 (Mac-2 antigen): defining molecular switches of affinity to natural glycoproteins, structural and dynamic aspects of glycan binding by flexible ligand docking and putative regulatory sequences in the proximal promoter region Biochim Biophys Acta 2011 1810:150-161 10.1016/j.bbagen.2010.11.001

4* Sahakyan AB, Vranken WF, Cavalli A, Vendruscolo M. Using Side-Chain Aromatic Proton Chemical Shifts for a Quantitative Analysis of Protein Structures Angew Chem Int Ed Engl 2011 50:9620-9623 10.1002/anie.201101641

3 Moreno-Morcillo M, Minvielle-Sébastia L, Fribourg S, Mackereth CD Locked Tether Formation by Cooperative Folding of Rna14p Monkeytail and Rna15p Hinge Domains in the Yeast CF IA Complex Structure 2011 19:534-545 10.1016/j.str.2011.02.003

2* Lange A, Hoeller D, Wienk H, Marcillat O, Lancelin JM, Walker O NMR Reveals a Different Mode of Binding of the Stam2 VHS Domain to Ubiquitin and Diubiquitin Biochemistry 2011 50:48–62 10.1021/bi101594a

1* Leineweber S, Schönig S, Seeger K Insight into interactions of the von-Willebrand-factor-A-like domain 2 with the FNIII-like domain 9 of collagen VII by NMR and SPR FEBS Lett 2011 585:1748-1752 10.1016/j.febslet.2011.04.071

 

*  Acknowledges e-NMR

** Acknowledges (both) e-NMR and WeNMR

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

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The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life