CAPRI communitywide experiment on the comparative evaluation of protein-protein docking for structure prediction
Hosted By EMBL/EBI-PDBe Group
Capri Target Publications, Please use in citing CAPRI work
| Target | Contributor | Protein Name | Startng PDB Entries | PDB final |
Reference |
Download Starting File |
| T01 | Sonia Fieulaine and Joel Janin (LEBS-CNRS, Gif-sur-Yvette, France) | HPr/Phosphovcarrier | 1SPH, 1JB1 | 1KKL |
Fieulaine S, Morera S, Poncet S, Mijakovic I, Galinier A,
Janin J, Deutscher J, Nessler S. X-ray structure of a
bifunctional protein kinase in complex with its protein substrate
Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13437-41. |
capri_01.brk |
| T02 | Felix Rey, Marie-Christine Vaney (LVMS-CNRS Gif-sur-Yvette) |
bovine rotavirus VP6 - Fab |
1QHD | ? | To Be Published |
capri_02.brk |
| T03 | Carole Martin and M. Knossow (LEBS-CNRS, Gif-sur-Yvette, France) | flu hemagglutinin - Fab HC63 |
? | 1KEN |
Barbey-Martin C, Gigant B, Bizebard T, Calder LJ, Wharton SA, Skehel JJ, Knossow M.
An antibody that prevents the hemagglutinin
low pH fusogenic transition.
Virology. 2002 Mar 1;294(1):70-4.
|
capri_03.brk |
| T04 | Christian Cambillau (AFMB-CNRS, Marseille, France) | alpha-amylase complex camelide antibody VH domain 1 |
1DHK | 1KXT |
Desmyter A, Spinelli S, Payan F, Lauwereys M, Wyns L, Muyldermans S, Cambillau C.
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
J Biol Chem. 2002 Jun 28;277(26):23645-50
|
capri_04.brk |
| T05 | Christian Cambillau (AFMB-CNRS, Marseille, France) | alpha-amylase complex camelide antibody VH domain 2 |
1DHK | 1KXV |
Desmyter A, Spinelli S, Payan F, Lauwereys M, Wyns L, Muyldermans S, Cambillau C.
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
J Biol Chem. 2002 Jun 28;277(26):23645-50
|
capri_05.brk |
| T06 | Christian Cambillau (AFMB-CNRS, Marseille, France) | alpha-amylase complex camelide antibody VH domain 3 |
1DHK | 1KXQ |
Desmyter A, Spinelli S, Payan F, Lauwereys M, Wyns L, Muyldermans S, Cambillau C.
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
J Biol Chem. 2002 Jun 28;277(26):23645-50
|
capri_06.brk |
| T07 | Roy Mariuzza carb.nist.gov | T cell receptor beta chain/ pyrogenic exotoxin A (SpeA) |
? | 1L0X |
Sundberg EJ, Li H, Llera AS, McCormick JK, Tormo J, Schlievert PM, Karjalainen K, Mariuzza RA.
Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes.
Structure. 2002 May;10(5):687-99.
|
capri_07.brk |
| T08 | Timothy A. Springer (Harvard Medical School) | Nidogen-G3/laminin |
? | 1NPE |
Takagi J, Yang Y, Liu JH, Wang JH, Springer TA.
Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface.
Nature. 2003 Aug 21;424(6951):969-74.
|
capri_08.brk |
| T09 | Herman van Tilbeurgh (Orsay) | Wild type LicT homodimer |
? | ? |
Graille M, Zhou CZ, Receveur-Brechot V, Colinet B, Declerck N,
van Tilbeurgh H. Activation of the LicT transcriptional antiterminator
involves a domain swing/lock mechanism provoking
massive structural changes. J Biol Chem. 2005 |
capri_09.brk |
| T10 | Felix Rey and Stephane Bressanelli (LVMS-CNRS, Gif-sur-Yvette, France) | Trimeric form of the TBEV envelope protein |
? | 1URZ |
Bessanelli et al. EMBO J 23:728-738 (2004) |
capri_10.brk |
| T11 | Maria J. Romao and Ana Luisa Carvalho (New University of Lisbon), José A.M. Prates, Luís M.A. Ferreira and Carlos M.G.A. Fontes (Technical University of Lisbon) | Cellulosome cohesin-dockerin complex (unbound-homology model) |
? | 1OHZ |
A.L.Carvalho,F.M.Dias,J.A.Prates,T.Nagy, H.J.Gilbert,G.J.Davies,
L.M.Ferreira,M.J.Romao,C.M.Fontes, Cellulosome assembly revealed
by the crystal. Structure of the cohesin-dockerin complex.
Proc.Natl.Acad.Sci.USA, 100 13809 2003 |
capri_11.brk |
| T12 | Maria J. Romao and Ana Luisa Carvalho (New University of Lisbon), José A.M. Prates, Luís M.A. Ferreira and Carlos M.G.A. Fontes (Technical University of Lisbon) | Cellulosome cohesin-dockerin complex (unbound/bound) |
? | 1OHZ |
A.L.Carvalho,F.M.Dias,J.A.Prates,T.Nagy, H.J.Gilbert,G.J.Davies,
L.M.Ferreira, M.J.Romao,C.M.Fontes, Cellulosome assembly revealed
by the crystal. Structure of the cohesin-dockerin complex.
Proc.Natl.Acad.Sci.USA, 100 13809 2003 |
capri_12.brk |
| T13 | Marc Graille, Frederic Ducancel (CEA Saclay, France) | SAG1-antibody complex (unbound/bound) |
? | 1YNT |
Graille M, Stura EA, Bossus M, Muller BH, Letourneur O, Battail-Poirot N, Sibaï G, Gauthier M, Rolland D, Le Du MH, Ducancel F.
Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response.
J Mol Biol. 2005 Nov 25;354(2):447-58.
|
capri_13.brk |
| T14 | Roberto Dominguez (Boston Biomedical Research Institute) | phosphatase-1/myosin phosphatase targeting subunit 1 |
? | 1S70 |
M. Terrak, F. Kerff, K. Langsetmo, T. Tao R. Dominguez Structural
basis of protein phosphatase 1 regulation Nature V. 429 780 2004 |
capri_14.brk |
| T15 | Marc Graille and Herman van Tilbeurgh (Gif-sur-Yvette) | ImmD-ColD |
? | 1V74 |
M.Graille,L.Mora,R.H.Buckingham,H.van Tilbeurgh,M.de Zamaroczy.
Structural inhibition of the colicin d trnase by
the trna-mimicking immunity protein EMBO J.23 1474 2004 |
capri_15.brk |
| T16 | Alain Roussel (AFMB, Marseille, France) | XIP-1/xylanase |
? | 1TA3 |
F.Payan,P.Leone,S.Porciero,C.Furniss,T.Tahir,G.Williamson,
A.Durand,P.Manzanares,H.J.Gilbert,N.Juge,A.Roussel
The dual nature of the wheat xylanase protein inhibitor
xip-i: structural basis for the inhibition of family 10
and family 11 xylanases. J.Biol.Chem 279 36029 2004 |
capri_16.brk |
| T17 | Alain Roussel (AFMB, Marseille, France) | XIP-1 xylanase inhibitor / xylanase |
? | 1TE1 |
F.Payan,P.Leone,S.Porciero,C.Furniss,T.Tahir,G.Williamson,
A.Durand,P.Manzanares,H.J.Gilbert,N.Juge,A.Roussel
The dual nature of the wheat xylanase protein inhibitor
xip-i: structural basis for the inhibition of family 10
and family 11 xylanases. J.Biol.Chem 279 36029 2004 |
capri_17.brk |
| T18 | Stefaan Sansen, Anja Rabijns (Leuven, Belgium) | TAXI/Xylanase |
? | 1T6G |
Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A.
Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I.
J Biol Chem. 2004 Aug 20;279(34):36022-8.
|
capri_18.brk |
| T19 | M. Knossow LEBS-CNRS, Gif-sur-Yvette, France | Ovine prion-FAB complex |
? | ? |
F.Eghiaian,J.Grosclaude,S.Lesceu,P.Debey,B.Doublet,
E.Treguer,H.Rezaei,M.Knossow
PNAS 101:10254 2004 |
capri_19.brk |
| T20 | M. Graille, H. van Tilbeurgh (Universit Paris-Sud,Orsay, France) | HemK/eRF1 |
? | 2B3T |
Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N,
Ulryck N, van Tilbeurgh H Buckingham RH.
Molecular basis for bacterial class I release factor
methylation by PrmC.Mol Cell. 2005 20:917-27. |
capri_20.brk |
| T21 | Jim Keck (University of Wisconsin, Madison, USA) | Orc1/Sir1 |
? | 1ZHI |
Hou Z, Bernstein DA, Fox CA, Keck JL.
Structural basis of the Sir1-origin recognition
complex interaction in transcriptional silencing
PNAS 2005 102:8489-94. |
capri_21.brk |
| T22 | Tine K. Nielsen (Max Planck Institut, Gottingen, Germany). | U5-15K/U5-52 |
? | 1SYX |
Nielsen, T.K., Liu, S., Luhrmann, R., Ficner, R.
The crystal structure of a binary U5 snRNP complex
Structural Basis for the Bifunctionality of the U5 snRNP
52K Protein (CD2BP2).
J Mol Biol. 2007 Apr 4; [Epub ahead of print] |
capri_22.brk |
| T23 | Louis Renault (LEBS-CNRS, Gif-sur-Yvette, France) | GBP1 dimer |
? | 2B8W |
Ghosh A, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C.
How guanylate-binding proteins achieve assembly-stimulated
processive cleavage of GTP to GMP.
Nature 2006 440:101-4. |
capri_23.brk |
| T24 | Julie Ménétrey (Institut Curie, Paris, France) | Arf1/ARHGap10 |
? | 2J59 |
J.Ménétrey, M.Perderiset, J.Cicolari, T.Dubois, N.Elkhatib,
F.El Khadali, M.Franco, P.Chavrier, A.Houdusse
Structural basis for ARF1-mediated recruitment of ARHGAP21
to Golgi membranes. EMBO J. 2007 in press. |
capri_24.brk |
| T25 | Julie Ménétrey (Institut Curie, Paris, France) | Arf1/ARHGap10 |
? | 2J59 |
J.Ménétrey, M.Perderiset, J.Cicolari, T.Dubois, N.Elkhatib,
F.El Khadali, M.Franco, P.Chavrier, A.Houdusse
Structural basis for ARF1-mediated recruitment of ARHGAP21
to Golgi membranes. EMBO J. 2007 in press. |
capri_25.brk |
| T26 | Colin Kleanthous (University of York, UK) | TolB/Pal |
? | 2HQS |
D.A.Bonsor,I.Grishkovskaya,E.J.Dodson,C.Kleanthous
Molecular mimicry enables competitive recruitment by a natively
disordered protein.
J.AM.CHEM.SOC. 129 4800 2007 |
capri_26.brk |
| T27 | John Walker (University of Toronto, Canada) | E2-25K/Ubc9 |
? | 2O25 |
Walker, J.R., Avvakumov, G.V., Xue, S., Newman, E.M.,
Mackenzie, F., Weigelt, J.,Sundstrom, M., Arrowsmith, C.H.,
Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.
A Novel and Unexpected Complex Between the SUMO-1-Conjugating
Enzyme UBC9 and the Ubiquitin-Conjugating Enzyme E2-25 kDa
(to be published)
| capri_27.brk |
| T28 | John Walker (University of Toronto, Canada) | E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE PROTEIN |
? | 2ONI |
T28 E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE PROTEIN
Reference: J.R.Walker,G.V.Avvakumov,S.Xue,C.Butler-Cole,J.Weigelt,
M.Sundstrom,C.H.Arrowsmith,A.M.Edwards,A.BOCHKAREV,S.Dhe-Paganon
NEDD4-LIKE E3 UBIQUITIN-PROTEIN LIGASE
(to be published)
Contributed by: John Walker (University of Toronto, Canada)
| capri_28.brk |
| T29 | Nicolas Leulliot and Herman Van Tilbeurgh (IBBMC,Orsay, France) | Trm8/Trm82 tRNA guanine-N(7)-methyltransferase from S. cerevisiae. |
? | 2VDU, 2VDV |
Leulliot N, Chaillet M, Durand D, Ulryck N, Blondeau K, van Tilbeurgh H.
Structure of the yeast tRNA m7G methylation complex.
Structure. 2008 Jan;16(1):52-61
|
capri_29.brk |
| T30 | W. Tempel, Y. Tong, H. Park and C. Arrowsmith
(Structural Genomics Consortium, Toronto, Ontario) | crystal structure
of Rnd1-GTP bound to the RBD dimer |
? | 2R20 |
Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M.
Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain.
J Biol Chem. 2007 Dec 21;282(51):37215-24.
|
capri_30.brk |
| T31 | P. Chugha and M. Buck (Case Western Reserve University,
Cleveland, Ohio) | NMR structure of Rac1-GTP (1mh1) in complex with
the RBD monomer. Y. Tong and M. Buck also determined a NMR structure
for the free RBD monomer |
? | 2JPH | |
capri_31.brk |
| T32 | Dr. Leonardo de Maria and Pernille Michelsen (Novozymes, Bagsvaerd, Danemark) |
a complex between the protease savinase (1SVN) and the bifunctional inhibitor BASI (1AVA_C) |
? | 3BX1 |
Micheelsen PO, Vevodova J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjot M
Journal of Molecular Biology, Volume 380, Issue 4, 18 July 2008, Pages 681-690 |
capri_32.brk |
| T33 | protein/RNA complex L. Renault (LEBS-CNRS, Gif-sur-Yvette, France) |
? |
? | ? |
? |
? |
| T34 | protein/RNA complex L. Renault (LEBS-CNRS, Gif-sur-Yvette, France) |
? |
? | ? |
? |
? |
| T35 | S. Najmudin and C. Fontes (Universidade Nova de Lisboa, Portugal) |
BM22-1- GH10 modules of Clostridium Xyn10B xylanase |
? | 2W5F |
Najmudin S, Pinheiro BA, Prates JAM, Romao MJ, Fontes CMGA (2010).
Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystallographic structure of the CBM22-1-GH10 modules complexed with xylohexaose.
S Najmudin, BA Pinheiro, JAM Prates, HJ Gilbert, MJ Romão, CMGA Fontes
Journal of Structural Biology (2010) 172: Pages353-362
|
capri_35.brk |
| T36 | S. Najmudin and C. Fontes (Universidade Nova de Lisboa, Portugal) |
BM22-1- GH10 modules of Clostridium Xyn10B xylanase |
? | 2W5F |
Najmudin S, Pinheiro BA, Prates JAM, Romao MJ, Fontes CMGA (2010).
Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystallographic structure of the CBM22-1-GH10 modules complexed with xylohexaose.
S Najmudin, BA Pinheiro, JAM Prates, HJ Gilbert, MJ Romão, CMGA Fontes
Journal of Structural Biology (2010) 172: Pages353-362 |
capri_36.brk |
| T37 | Dr. Julie Ménetrey (Institut Curie, Paris) |
ARF-EFFECTOR COMPLEX |
? | 2W83 |
Isabet, T., Montagnac, G., Regazzoni, K., Raynal, B., Elkhadali, F., Franco, M., England, P., Chavrier, P., Houdusse, A., Menetrey, J.
(2009) EMBO J. 28:2835-45
|
capri_37.brk |
| T38 | Centaurin-alpha1/FHA domain of KIF13B H.W. Park (Structural Genomics Consortium, Toronto) |
Centaurin-alpha1/FHA domain COMPLEX |
? | 3FM8 |
|
capri_38.brk |
| T39 | Centaurin-alpha1/FHA domain of KIF13B H.W. Park (Structural Genomics Consortium, Toronto) |
Centaurin-alpha1/FHA domain COMPLEX |
? | 3FM8 |
|
capri_39.brk |
| T40 | Trypsin/API-A R. Bao & Y. Chen (USTC, Hefei, Anhui, China) |
bovine trypsin and protease inhibitor (API-A) COMPLEX |
? | 3E8L |
BaoR, Zhou ZC, Jiang C, Lin SX, Chi CW, Chen Y (2009).
The ternary structure of double-headed arrowhead protease inhibitor
API-A complexed with two trypsins reveals a novel reactive site conformation
J Biol Chem. 284:26676-84 |
capri_40.brk |
| T41 | Colicin E9/Im2 N. Meenan and C Kleanthous (York University, UK) |
Colicin E9 DNase and Im2 immunity protein |
? | 2WPT |
Meenan NAG, Sharma A, Fleishman SJ, MacDonald C, Morel B, Boetzel R, Moore GR, Baker D, Kleanthous C (2010)
The structural and energetic basis for high selectivity in a high affinity protein-protein interaction.
Proc. Natl. Acad. Sci. USA 107:10080-85
| capri_41.brk |
| T42 | Designed TPR trimer C Kleanthous (York University, UK) |
Oligomeric assembly of a designed tetratricopeptide (Note that the oligomer is created by crystal symmetries) |
? | 2WQH |
Krachler AM, Sharma A, Kleanthous C (2010).
Self-association of TPR-domains: natural and engineered.
Proteins, Published Online: Mar 23 DOI: 10.1002/prot.22726, Proteins 78:2131-43
| capri_42.brk |
| T43 | Designed complexes, scoring only (D. Baker & S. Fleishman, University of Washington) |
|
? | ? |
Fleishman et al. (2011)
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
J. Mol. Biol. 414:289
| capri_43.brk |
| T44 | Designed complexes, scoring only (D. Baker & S. Fleishman, University of Washington) |
|
? | ? |
Fleishman et al. (2011)
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
J. Mol. Biol. 414:289
| capri_44.brk |
| T45 | Designed complexes, scoring only (D. Baker & S. Fleishman, University of Washington) |
|
? | ? |
Fleishman et al. (2011)
Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
J. Mol. Biol. 414:289
| ? |
| T46 | Methyl transferase Mtq2/Trm112 (M. Graille, Université Paris-Sud, Orsay) |
? |
? | 3Q87 |
Liger et al. (2011)
Mechanism of activation of methyltransferases involved in translation by the Trm112 'hub' protein.
Nuc. Ac. Res. 39:6249.
| capri_46.brk |
| T50 | HB36.3 designed protein / flu hemagglutinin (D. Baker & S. Fleishman, University of Washington) |
? |
? | 3R2X |
Fleishman et al. (2011)
Computational design of proteins targeting the conserved stem region of influenza hemagglutinin.
Science 332:816-21
| capri_50.brk |
| T51 | Xylanase Xyn10B (S. Najmudin, University of Lisbon) |
? |
? | 2W5F |
Najmudin et al. (2010).
Putting an N-Terminal End to the Clostridium Thermocellum Xylanase Xyn10B Story: Crystal Structure of the Cbm22-1-Gh10 Modules Complexed with Xylohexaose.
J.Struct.Biol. 172: 353.
| capri_51.brk |
Email Problems or Queries to Sameer Velankar
|
