HADDOCK

HADDOCK-related publications

This page lists haddock development articles and a selection of papers in which HADDOCK has been be used to generate models of biomolecular complexes.

HADDOCK development papers

The original JACS paper, together with an introduction to the study of biomolecular complexes and an application to the UbcH5-CNOT4 complex can be found online in Cyril Dominguez's Ph.D. thesis:

When using HADDOCK cite:

and, if used, cite in addition any publication related to the use of RDCs, diffusion anisotropy data, protein-DNA docking and/or solvated docking (see below).

The use of residual dipolar couplings in HADDOCK is described in:

The use of diffusion anisotropy data in HADDOCK is described in:

Solvated docking using HADDOCK is described in:

Flexible protein-DNA docking using HADDOCK is described in:

Our results in CAPRI, the blind docking experiment, are described in (Note that entire issues of Protein are dedicated to CAPRI):

The following review on data-driven docking is freely available for download:


Protein-protein complexes

  1. D. Owen, P.N. Lowe, D. Nietlispach, C.E. Brosnan, D.Y. Chirgadze, P.J. Parker, T.L. Blundell and H.R. Mott
    "Molecular dissection of the interaction between the small G proteins Rac1 and RhoA and protein kinase C-related kinase 1 (PRK1)."
    J. Biol. Chem., 278 50578-5087 (2003).

  2. A. van Drogen-Petit, C. Zwahlen, M. Peter and A.M.J.J. Bonvin
    "Insight into molecular interactions between two PB1 domains."
    J. Mol. Biol., 336/5 1195-1210 (2004).

  3. T.D. Mueller, M. Kamionka and J. Feigon
    "Specificity of the interaction between ubiquitin-associated domains and ubiquitin."
    J. Biol. Chem., 279 11926-11936 (2004).

  4. F. Arnesano, L. Banci, I. Bertini and A.M.J.J. Bonvin
    "A docking approach to the study of copper trafficking proteins: interaction between metallochaperones and soluble domains of copper ATPases."
    Structure, 12 669-676 (2004).

  5. C. Dominguez, A.M.J.J. Bonvin, G.S. Winkler, F.M.A. van Schaik, H.Th.M. Timmers and R.Boelens
    "Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis and docking approaches."
    Structure, 12 633-644 (2004).

  6. X.M. Yuan, P. Simpson, C. Mckeown, H. Kondo, K. Uchiyama, R. Wallis, I. Dreveny, C. Keeth, X.D. Zhang, C. Robinson, P. Freemont and S. Matthews
    "Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97."
    EMBO J. 23(7) 1463-1473 (2004).

  7. M.E. Stauffer and W.J. Chazin
    "Physical Interaction between Replication Protein A and Rad51 Promotes Exchange on Single-stranded DNA"
    J. Biol. Chem. 279(24) 25638-25645 (2004).

  8. R.J.Y. Simpson, S.H.Y. Lee, N. Bartle, E.Y. Sum, J.E. Visvader, J.M. Matthews, J.P. Mackay and M. Crossley
    "A Classic Zinc Finger from Friend of GATA Mediates an Interaction with the Coiled-coil of Transforming Acidic Coiled-coil 3."
    J. Biol. Chem.,279, 39789-39797 (2004).

  9. B. Dangi, A.M. Gronenborn, J.L. Rosner and R.G. Martin
    "Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use the DNA contact site as a protein contact site for MarA."
    Mol. Microbiol.,54, 45-59, (2004).

  10. N.U. Jain, T.J. Wyckoff, C.R. Raetz, J.H. Prestegard
    "Rapid Analysis of Large ProteinProtein Complexes Using NMR-derived Orientational Constraints: The 95 kDa Complex of LpxA with Acyl Carrier Protein."
    J. Mol. Biol.,343, 1379-1389 (2004).

  11. B.J. Westman, J.Perdomo, J.M. Matthews, M. Crossley, and J.P. Mackay
    "Structural Studies on a Protein-Binding Zinc-Finger Domain of Eos Reveal Both Similarities and Differences to Classical Zinc Fingers."
    Biochemistry, 43, 13318-13327 (2004).

  12. B.K. Sharpe, C.K. Liew, A.H. Kwan, J.A. Wilce, M. Crossley, J.M. Matthews and J.P. Mackay
    "Assessment of the Robustness of a Serendipitous Zinc Binding Fold: Mutagenesis and Protein Grafting."
    Structure, 13, 257-266 (2005).

  13. A.N. Volkov, D. Ferrari, J.A.R. Worrall, A.M.J.J. Bonvin and M. Ubbink
    "The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK."
    Protein Science, 14, 799-811 (2005).

  14. R. Varadan, M. Assfalg, S. Raasi, C. Pickart and D. Fushman
    "Structural Determinants for Selective Recognition of a Lys48-Linked Polyubiquitin Chain by a UBA Domain"
    Mol. Cell 18, 687-698 (2005).

  15. I. Diaz-Moreno, A. Diaz-Quintana, M. Ubbink and M.A. De la Rosa
    "An NMR-based docking model for the physiological transient complex between cytochrome f and cytochrome c6"
    FEBS Letters 579, 2891-2896 (2005).

  16. G. Nicastro, R.P. Menon, L. Masino, P.P. Knowles, N.Q. McDonald, and A. Pastore
    "The solution structure of the Josephin domain of ataxin-3: Structural determinants for molecular recognition"
    PNAS 102,10493-10498 (2005).

  17. S. Deep, S.-C. Im, E.R.P. Zuiderweg and L. Waskell
    "Characterization and Calculation of a Cytochrome c-Cytochrome b5 Complex Using NMR Data"
    Biochemistry 44, 10654-10668 (2005).

  18. O. Hantsche, S. Wiesner, T. Guttler, C.D. Mackereth, L.L. Remsing Rix, Z. Mikes, J. Dehne, D. Gorlich, M. Sattler and G. Superti-Furga
    "Structural Basis for the Cytoskeletal Association of Bcr-Abl/c-Abl"
    Mol. Cell. 19, 461-473 (2005).

  19. V. Nogueraa, O. Walker, N. Rouhier, J.-P. Jacquot, I. Krimm and J.-. Lancelin
    "NMR Reveals a Novel GlutaredoxinGlutaredoxin Interaction Interface"
    J. Mol. Biol. 353, 629-641 (2005).

  20. B. Card, P.J.A. Erbel and K.H. Gardner
    "Structural Basis of ARNT PAS-B Dimerization: Use of a Common Beta-sheet Interface for Hetero- and Homodimerization"
    J. Mol. Biol. 353, 664-677 (2005).

  21. C.K. Liew, R.J.Y. Simpson, A.H.Y. Kwan, L.A. Crofts, F.E. Loughlin, J.M. Matthews, M. Crossley and J.P. Mackay
    "Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/Friend of GATA interaction"
    PNAS 102,583-588 (2005).

  22. I. Bertini, G. Cavallaro and A. Rosato
    "A structural model for the adduct between cytochrome c and cytochrome c oxidase."
    J. Biol. Inorg. Chem. 10,613-624 (2005).

  23. S.J. Zhang, Z.M. Hu and W.D. Chen Y
    "Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif - A reversal of the bound orientation."
    J. Biol. Chem. 280,40122-40129 (2005).

  24. H.S. Ding, Y.D. Yang, J.H. Zhang, J.H. Wu, H.T. Liu HY, Y.Y. Shi
    "Structural basis for SUMO-E2 interaction revealed by a complex model using docking approach in combination with NMR data."
    Proteins 61, 1050-1058 (2005).

  25. L.P. Yu, C.H. Sun, D.Y. Song, J.W. Shen, N. Xu, A. Gunasekera, P.J. Hajduk and E.T. Olejniczak
    "Nuclear magnetic resonance structural studies of a potassium channel-charybdotoxin complex."
    Biochemistry 44, 15834-15841 (2005).

  26. B.E. Correia, N. Loureiro-Ferreira, J.R. Rodrigues and R.M.M. Brito
    "A structural model of an amyloid protofilament of Transthyretin."
    Prot. Sci. 15, 28-32 (2006).

  27. B.O. Smith, N.C. Picken, G.D. Westrop, K. Bromek, J.C. Mottram and G.H. Coombs
    "The Structure of Leishmania mexicana ICP Provides Evidence for Convergent Evolution of Cysteine Peptidase Inhibitors."
    J. Biol. Chem. 281, 5821-5828 (2006).

  28. M.J. Lewis, L.F. Saltibus, D.D. Hau, W. Xiao and L.o Spyracopoulos
    "Structural Basis for Non-Covalent Interaction Between Ubiquitin and the Ubiquitin Conjugating Enzyme Variant Human MMS2."
    J. Biomol. NMR. 34, 89-100 (2006).

  29. L. Muresanu, P. Pristovsek, F. Loehr, O. Maneg, M.D. Mukrasch, H. Ruterjans, B. Ludwig and C. Luecke
    "The electron transfer complex between cytochrome C552 and the CuA domain of the Thermophilus ba3 oxidase - a combined NMR and computational approach."
    J. Biol. Chem., advanced online publication (2006).

  30. X. Zhang, Y. Hu, X. Guo, E. Lescop, Y. Li, B. Xia and C. Jin
    "The Bacillus subtilis YkuV Is a Thiol:Disulfide Oxidoreductase Revealed by Its Redox Structures and Activity."
    J. Biol. Chem., 281, 8296-8304 (2006).

  31. A. Koglin, M.R. Mofid, F. Löhr, B. Schäfer, V.V. Rogov, M.-M. Blum, T. Mittag, M.A. Marahiel, F. Bernhard, V. Dötsch
    "Conformational Switches Modulate Protein Interactions in Peptide Antibiotic Synthetases."
    Science, 312, 273-276 (2006).

  32. Y.G. Chang, A.X. Song, Y.C. Gao, Y.H. Shi, X.J. Lin, X.T. Cao, D.H. Lin and H.Y. Hu
    "Solution structure of the ubiquitin-associated domain of human BMSC-UbP and its complex with ubiquitin."
    Protein Science 15 1248-1259 (2006).

  33. L. Banci, I. Bertini, S. Ciofi-Baffoni, N.G. Kandias, N.J. Robinson, G.A. Spyroulias, X.-C. Su, S. Tottey and M. Vanarotti
    "The delivery of copper for thylakoid import observed by NMR"
    Proc. Natl. Acad. Sci. 103 8320-8325 (2006).

  34. A.P. Herbert, D. Uhrin, M. Lyon, M.K. Pangburn and P.N. Barlow
    "Disease-associated Sequence Variations Congregate in a Polyanion Recognition Patch on Human Factor H Revealed in Three-dimensional Structure"
    J. Biol. Chem., 281, 16512-16520 (2006).

  35. M. Slutzkia, D.A. Jaitina, T.B. Yehezkela and G. Schreiber
    "Variations in the Unstructured C-terminal Tail of Interferons Contribute to Differential Receptor Binding and Biological Activity."
    J. Mol. Biol., 360, 1019-1030 (2006).

  36. S.R. Quadt-Akabayov, J.H. Chill, R. Levy, N. Kessler and J. Anglister
    "Determination of the human type I interferon receptor binding site on human interferon-?2 by cross saturation and an NMR-based model of the complex."
    Prot. Sci, 15, 2656-2668 (2006).

  37. Z. Lin, S. Sriskanthadevan, H. Huang, C.-H. Siu and D. Yang
    "Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca2+-dependent cell-cell adhesion."
    Nat. Struc. Mol. Biol., 13, 1016-1022 (2006).

  38. B. Zhou, J. Zhang, S. Liu, S. Reddy, F. Wang and Z.-Y. Zhang
    "Mapping ERK2-MKP3 Binding Interfaces by Hydrogen/Deuterium Exchange Mass Spectrometry."
    J. Biol. Chem., 281, 38834-38844 (2006).

  39. G.A. Jensen, O.M. Andersen, A.M.J.J. Bonvin, I. Bjerrum-Bohr, M. Etzerodt, H.C. Thogersen, F.M. Poulsen1 and B.B. Kragelund
    "Binding Site Structure of One LRP/RAP Complex -Implications for a Common Ligand/Receptor Binding Motif."
    J. Mol. Biol., 362 700-716 (2006).

  40. B. Rodamilans, I.G. Munoz, E. Bragado-Nilsson, M.R. Sarrias, O. Padilla, F.J. Blanco, F. Lozano and G. Montoya
    "Crystal structure of the third extracellular domain of CD5 reveals the fold of a group B scavenger cysteine-rich receptor domain."
    J. Biol. Chem., 282, 12669-12677 (2007).

  41. A.D.J. van Dijk, S. Ciofo-Bafoni, L. Banci, I. Bertini, R. Boelens and A. M. J. J. Bonvin
    "Modelling protein-protein complexes involved in the cytochrome c oxidase copper-delivery pathway."
    J. Proteome Research, 6 1530-1539 (2007).

  42. H. Da, N. Shen, D. Arac and J. Rizo
    "A Quaternary SNAREÐSynaptotagminÐCa2+ÐPhospholipid Complex in Neurotransmitter Release."
    J. Mol. Biol., 367, 848-863 (2007).

  43. W. Feng, H. Wu, L.-N. Chan and M. Zhang
    "The Par-3 NTD adopts a PB1-like structure required for Par-3 oligomerization and membrane localization."
    EMBO J., 26, 2786-2796 (2007).

  44. P. Gutierrez, G. Kozlov, L. Gabrielli, D. Elias, M.J. Osborne, I.E. Gallouzi and K. Gehring
    "Solution Structure of YaeO, a Rho-specific Inhibitor of Transcription Termination."
    J. Biol. Chem., 282, 23348-23353 (2007).

  45. J. Wang, W. Hu, S. Cai, B Lee, J. Song and Y. Chen
    "The Intrinsic Affinity between E2 and the Cys Domain of E1 in Ubiquitin-like Modifications."
    Mol. Cell, 27, 228-237 (2007).

  46. R.J.M. Abbott, I. Spendlove, P. Roversi, H. Fitzgibbon, V. Knott, P. Teriete, J.M. McDonnell, P.A. Handford and S.M. Lea
    "Structural and Functional Characterization of a Novel T Cell Receptor Co-regulatory Protein Complex, CD97-CD55."
    J. Biol. Chem., 282, 22023-22032 (2007).

  47. A. Fontayne, B. De Maeyer, M. De Maeyer, M. Yamashita, T. Matsushita and H. Deckmyn
    "Paratope and Epitope Mapping of the Antithrombotic Antibody 6B4 in Complex with Platelet Glycoprotein Ibalpha."
    J. Biol. Chem., 282 23517-23524 (2007).

  48. C. Williams, D. Rezgui, S.N. Prince, O.J. Zaccheo, E.J. Foulstone, B.E. Forbes, R.S. Norton, J. Crosby, A. Bassim Hassan and M.P. Crump
    "Structural Insights into the Interaction of Insulin-like Growth Factor 2 with IGF2R Domain 11."
    Structure, 15 1065-1078 (2007).

  49. A. Abadou, M. Gautel and M. Pfuhl
    "Disecting the N-terminal myosin binding site of human cardiac myosin binding protein C : Structure and myosin binding of domain C2."
    J. Biol. Chem., 282 9204-9215 (2007).

  50. C. Pimentel, S. M'Barek, V. Visan, S. Grissmer, F. Sampieri, J.-M. Sabatier, H. Darbon and Z. Fajloun
    "Chemical synthesis and 1H-NMR 3D structure determination of AgTx2-MTX chimera, a new potential blocker for Kv1.2 channel, derived from MTX and AgTx2 scorpion toxins."
    Prot Sci., 17 107-118 (2008).

  51. N. Korotkova, Y. Yang, I. Le Trong, E. Cota, B. Demeler, J. Marchant, W.E. Thomas, R.E. Stenkamp, S.L. Moseley and S. Matthews
    "Binding of Dr adhesins of Escherichia coli to carcinoembryonic antigen triggers receptor dissociation"
    Mol. Microbio., 67 420-434 (2008).

  52. A.R. Diaz, S. Stephenson, J.M. Green, V.M. Levdikov, A.J. Wilkinson and M. Perego
    "Functional role for a conserved aspartate in the Spo0E signature motif involved in the dephosphorylation of the bacillus subtilis sporulation regulator Spo0A."
    J. Biol. Chem., 283 2962-2972 (2008).

  53. K. Seidel, O.C. Andronesi, J. Krebs, C. Griesinger, H.S. Young, S. Becker and M. Baldus
    "Structural Characterization of Ca2+-ATPase-Bound Phospholamban in Lipid Bilayers by Solid-State Nuclear Magnetic Resonance (NMR) Spectroscopy."
    Biochemistry, 47 4369-4376 (2008).

  54. E. Ceraudo, S. Murail, Y.-V. Tan, J.-J. Lacapere, J.-M. Neumann, A. Couvineau and M. Laburthe
    "The Vasoactive Intestinal Peptide (VIP) {alpha}-Helix Up to C Terminus Interacts with the N-Terminal Ectodomain of the Human VIP/Pituitary Adenylate Cyclase-Activating Peptide 1 Receptor: Photoaffinity, Molecular Modeling, and Dynamics."
    Mol. Endo., 22 147-155 (2008).

Protein-peptide complexes

  1. G.H. Gao, K.C. Prutzman, M.L. King, D.M. Scheswohl, E.F. DeRose, R.E. London, M.D. Schaller and S.L. Campbell
    "NMR solution structure of the focal adhesion targeting domain of focal adhesion kinase in complex with a paxillin LD peptide - Evidence for a two-site binding model."
    J. Biol. Chem., 279 8441-8451 (2004).

  2. A.G. Tzakos, P. Fuchs, N.A.J. van Nuland, A. Troganis, T. Tselios, S. Deraos, J. Matsoukas, I.P. Gerothanassis and A.M.J.J. Bonvin
    "NMR and MD Studies of an Autoimmune MBP Peptide and its Antagonist. Structural Implications for the MHC II (I-Au) Peptide Complex through Docking Calculations."
    Eur. J. Biochem.,271, 3399-3413 (2004).

  3. B. Ritter, A.Y. Denisov, J. Philie, C. Deprez, E.C. Tung, K. Gehring and P.S. McPherson, PS
    "Two WXXF-based motifs in NECAPs define the specificity of accessory protein binding to AP-1 and AP-2."
    EMBO J., 23, 3701-3710 (2004).

  4. A.Y. Denisov, G. Chen, T. Sprules, T. Moldoveanu, P. Beauparlant and K. Gehring
    "Structural Model of the BCL-w-BID Peptide Complex and Its Interactions with Phospholipid Micelles."
    Biochemistry 45, 2250-2256 (2006).

  5. V. Musi, B. Birdsall, G. Fernandez-Ballester, R. Guerrini, S. Salvatori, L. Serrano, A. Pastore
    "New approaches to high-throughput structure characterization of SH3 complexes: The example of Myosin-3 and Myosin-5 SH3 domains from S-cerevisiae"
    Prot. Sci., 15, 795-807 (2006).

  6. A.P. Rideau, C. Gooding, P.J. Simpson, T.P. Monie, M. Lorenz., S. Hüttelmaier, R.H. Singer, S. Matthews, S. Curry and C.W.J. Smith
    "A peptide motif in Raver1 mediates splicing repression by interaction with the PTB RRM2 domain."
    Nat. Struc. Mol. Biol., 13, 839-848 (2006).

  7. K. Ma, J.G. Forbes, G. Gutierrez-Cruz and K. Wang
    "Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways."
    J. Biol. Chem., 281, 27539-27556 (2006).

  8. M.L. Reese, S. Dakoji, D.S. Bredt & V. Dötsch
    "The guanylate kinase domain of the MAGUK PSD-95 binds dynamically to a conserved motif in MAP1a."
    Nat. Struc. Mol. Biol., 14, 155-163 (2007).

  9. R.K. Mahadev, S.M. Di Pietro, J.M. Olson, H.L. Piao, G.S. Payne and M. Overduin
    "Structure of Sla1p homology domain 1 and interaction with the NPFxD endocytic internalization motif."
    EMBO J., 26, 1963-1971 (2007).

  10. S. Casares, E. AB, H. Eshuis, O. Lopez-Mayorga, N.A.J. van Nuland and F. Conejero-Lara
    "The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3."
    BMC Struc. Biol., 7, 22 (2007).

  11. Y. Wei, S. Liu, J. Lausen, C. Woodrell, S. Cho, N. Biris, N. Kobayashi, Y. Wei, S. Yokoyama and M.H. Werner
    "A TAF4-homology domain from the corepressor ETO is a docking platform for positive and negative regulators of transcription."
    Nat. Struct. Mol. Biol., 14, 653-661 (2007).

  12. I. Gelis, A.M.J.J. Bonvin, D. Keramisanou, M. Koukaki, G. Gouridis, S. Karamanou, A. Economou and C.G. Kalodimos
    "Structural basis for signal sequence recognition by the translocase motor SecA determined by NMR"
    Cell, 131, 756-769 (2007).

Protein-DNA/RNA complexes

  1. L. Volpon, I. D'Orso, C.R. Young, A.C. Frasch and K. Gehring
    "    NMR Structural Study of TcUBP1, a Single RRM Domain Protein from Trypanosoma cruzi: Contribution of a Hairpin to RNA Binding"
    Biochemistry 44, 3708-3717 (2005).

  2. M.B. Kamphuis, A.M.J.J. Bonvin, M.C. Monti, M. Lemonnier, A. Munoz-Gomez, R.H.H. van den Heuvel, R. Diaz-Orejas and R. Boelens
    "Model for RNA Binding and the Catalytic Site of the RNase Kid of the Bacterial parD Toxin-Antitoxin System."
    J. Mol. Biol., 357, 115-126 (2006).

  3. S. Singh, M.H. Hager, C. Zhang, B.R. Griffith, M. S. Lee, K. Hallenga, J.L. Markley and J. S. Thorson
    "Structural Insight into the Self-Sacrifice Mechanism of Enediyne Resistance."
    ACS Chem. Biol., 1, 451-460 (2006).

  4. H.R.A. Jonker, S. Ilin, S.K. Grimm, J. W&uouml;hnert and H. Schwalbe
    "L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy."
    Nucl. Acid Res., 35, 441-455 (2007).

  5. S. Cai, L. Zhu, Z. Zhang, and Y. Chen
    "Determination of the Three-Dimensional Structure of the Mrf2-DNA Complex Using Paramagnetic Spin Labeling."
    Biochemistry, 46, 4943-4950 (2007).

  6. W. Liu, G. Vierke, A.-K.n Wenke, . Thomm and R. Ladenstein
    "Crystal Structure of the Archaeal Heat Shock Regulator from Pyrococcus furiosus: A Molecular Chimera Representing Eukaryal and Bacterial Features"
    J. Mol. Biol., 369, 474-488 (2007).

  7. R. Gamsjaeger, M.K. Swanton, F.J. Kobus, E. Lehtomaki, J.A. Lowry, A.H. Kwan, J.M. Matthews and J.P. Mackay
    "Structural and Biophysical Analysis of the DNA Binding Properties of Myelin Transcription Factor 1."
    J. Biol. Chem., 283, 5158-5167 (2008).

  8. V.A. Burns, B.G. Bobay, A. Basso, J. Cavanagh, C. Melander
    "Targeting RNA with cysteine-constrained peptides."
    Bioorg. & Med. Chem. Letters, 18 565-567 (2008).

  9. D. Bessiere, C. Lacroix, S. Campagne, V. Ecochard, V. Guillet, L. Mourey, F. Lopez, J. Czaplicki, P. Demange, A. Milon, J.-P. Girard and V. Gervais
    "Structure-function analysis of the thap-zinc finger of thap1, a large C2CH DNA-binding module linked to RB/E2F pathways"
    J. Biol. Chem., 283, 4352-4363 (2008).

Protein-ligand complexes

  1. U. Schieborr, M. Vogtherr, B. Elshorst, M. Betz, S. Grimme, B. Pescatore, T. Langer, K. Saxena, H. Schwalbe
    "    How Much NMR Data Is Required To Determine a Protein-Ligand Complex Structure?"
    ChemBioChem 6, 1-9 (2005).

  2. L. Rutten, J. Geurtsen, W. Lambert, J.J. Smolenaers, A.M.J.J. Bonvin, A. de Haan, P. van der Ley, M.R. Egmond, P. Gros and J. Tommassen.
    "Crystal structure and catalytic mechanism of the LPS 3-O-deacylase PagL from Pseudomonas aeruginosa."
    Proc. Natl. Acad. Sci., 103 7071-7076-244 (2006).

  3. N. Zhang, L. Liu, F. Liu, C.R. Wagner, P.E. Hanna and K.J. Walters
    "NMR-based Model Reveals the Structural Determinants of Mammalian Arylamine N-Acetyltransferase Substrate Specificity."
    J. Mol. Biol., 363, 188-200 (2006).

  4. S. Singh, M.H. Hager, C. Zhang, B.R. Griffith, M. S. Lee, K. Hallenga, J.L. Markley and J. S. Thorson
    "Structural Insight into the Self-Sacrifice Mechanism of Enediyne Resistance."
    ACS Chem. Biol., 1, 451-460 (2006).

  5. J. Song, K.Q. Zhao, C.L. Loushin Newman, D.A. Vinarov and J.L. Markley
    "Solution structure of human sorting nexin 22."
    Prot. Sci., 16, 807-814 (2007).

  6. L. Mollica, F. De Marchis, A. Spitareli, C. Dallacosta, D. Pennacchini, M. Zmai, A. Agresti, L. Trisciuoglio, G. Musco and M.E. Bianchi
    "Glycyrrhizin Binds to High-Mobility Group Box 1 protein and Inhibits its Cytokine Activities."
    Chemistry & Biology, 14, 431-441 (2007).

  7. A. M. Wu, T. Singh, J.-H. Liu, M. Krzeminski, R. Russwurm, H.-C. Siebert, A. M. J. J. Bonvin, Sabine Andre, H.-J. Gabius
    "Activity-structure correlations in divergent lectin-evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16."
    Glycobiology, 17 165-184 (2007).

  8. S. Tomaselli, L. Ragona, L. Zetta, M. Assfalg, P. Ferranti, R. Longhi, A. M. J. J. Bonvin and H. Molinari.
    "NMR-based modeling and binding studies of a ternary complex between chicken liver bile acid binding protein and bile acids."
    Proteins: Struc. Funct. & Bioinformatic, 69 177-191 (2007).

  9. P. Barraud, B. Golinelli-Pimpaneau, C.c Atmanene, S. Sanglier, A. Van Dorsselaer, L. Droogmans, F. Dardel and C. Tisne
    "Crystal Structure of Thermus thermophilus tRNA m 1 A58 Methyltransferase and Biophysical Characterization of Its Interaction with tRNA."
    J. Mol. Biol., 347 535-550 (2008).

  10. V. Veverka, T. Crabbe, I. Bird, G. Lennie, F.W. Muskett, R.J. Taylor and M.D. Carr
    "Structural characterization of the interaction of mTOR with phosphatidic acid and a novel class of inhibitor: compelling evidence for a central role of the FRB domain in small molecule-mediated regulation of mTOR."
    Oncogene, 27 585-595 (2008).

Other complexes

  1. F. Dancea, K. Kami and M. Overduin
    "    Lipid Interaction Networks of Peripheral Membrane Proteins Revealed by Data-Driven Micelle Docking."
    Biophys. J., 94 515-524 (2008).