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CAPRI: Critical Assessment of PRediction of Interactions

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


TargetContributorProtein NameStartng PDB EntriesPDB final Reference Download Starting File
T01Sonia Fieulaine and Joel Janin (LEBS-CNRS, Gif-sur-Yvette, France)HPr/Phosphovcarrier1SPH, 1JB11KKL 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
T02Felix Rey, Marie-Christine Vaney (LVMS-CNRS Gif-sur-Yvette) bovine rotavirus VP6 - Fab 1QHD?To Be Published capri_02.brk
T03Carole 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.
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T04Christian Cambillau (AFMB-CNRS, Marseille, France)alpha-amylase complex camelide antibody VH domain 1 1DHK1KXT 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
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T05Christian Cambillau (AFMB-CNRS, Marseille, France)alpha-amylase complex camelide antibody VH domain 2 1DHK1KXV 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
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T06Christian Cambillau (AFMB-CNRS, Marseille, France)alpha-amylase complex camelide antibody VH domain 3 1DHK1KXQ 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
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T07Roy Mariuzza carb.nist.govT 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.
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T08Timothy 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.
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T09Herman 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
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T10Felix 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
T11Maria 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
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T12Maria 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
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T13Marc 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.
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T14Roberto 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
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T15Marc 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
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T16Alain 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
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T17Alain 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
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T18Stefaan 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.
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T19M. Knossow LEBS-CNRS, Gif-sur-Yvette, FranceOvine prion-FAB complex ?? F.Eghiaian,J.Grosclaude,S.Lesceu,P.Debey,B.Doublet,
E.Treguer,H.Rezaei,M.Knossow
PNAS 101:10254 2004
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T20M. 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.
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T21Jim 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.
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T22Tine 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]
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T23Louis 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.
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T24Julie 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.
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T25Julie 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.
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T26Colin 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
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T27John 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)
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T28John 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)
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T29Nicolas 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
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T30W. 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.
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T31P. 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
T32Dr. 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
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T33protein/RNA complex L. Renault (LEBS-CNRS, Gif-sur-Yvette, France) ? ?? ? ?
T34protein/RNA complex L. Renault (LEBS-CNRS, Gif-sur-Yvette, France) ? ?? ? ?
T35S. 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
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T36S. 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
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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
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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
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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
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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
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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
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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
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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, University 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.
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T47 a protein-protein complex (unbound/homology) - it is related to one in the PDB, and the position of interface solvent molecules should be predicted. ? ?3U43 Wojdyla JA, Fleishman SJ, Baker D, Kleanthous C (2012)
. Structure of the ultra-high-affinity colicin E2 DNase--Im2 complex.
J Mol Biol. 417:79-94.
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T48 T4moC /T4moH mono-oxygenase complex. JF Acheson, LJ Baily, BG Fox. Structure of a diiron hydroxylase ferredoxin electron transfer complex ? ?4I57 ? ?
T49 T4moC /T4moH mono-oxygenase complex. JF Acheson, LJ Baily, BG Fox. Structure of a diiron hydroxylase ferredoxin electron transfer complex ? ?4I57 Acheson JF, Bailey LJ, Fox BG. Structure of a diiron hydroxylase ferredoxin electron transfer complex, in preparation. ?
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
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T51 Xylanase Xyn10B (S. Najmudin, University of Lisbon) ? ?4BXG Bras JLA, Gilbert HJ, Ferreira LMA, Fontes CMGA, Najmudin S. The penta-modular cellulosomal arabinoxylanase CtXy15A structure as revealed by X-ray crystallography, in preparation. ?
T53 Designed Rep4/Rep2 a-repeat complex, by P. Minard and M. Graille (University Paris-Sud, France) ? ?4JW2 Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P.
Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)
PLOS One, published 27 Aug 2013 doi:10.1371/journal.pone.0071512.
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T54 Designed neocarzinostatin/Rep16 a-repeat complex, by P. Minard and M. Graille (University Paris-Sud, France) ? ?4JW3 Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P.
Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep)
PLOS One, published 27 Aug 2013 doi:10.1371/journal.pone.0071512.
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T55 (affinity prediction) Scoring mutants of a designed complex, by D. Baker, T. Whitehead and S.Fleishman (University of Washington, Seattle). ? ?4EEF Whitehead et al. (2012)
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.
Nat Biotechnol.30:543-548.
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T56 (affinity prediction) Scoring mutants of a designed complex, by D. Baker, T. Whitehead and S.Fleishman (University of Washington, Seattle). ? ?4EEF Whitehead et al. (2012)
Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.
Nat Biotechnol.30:543-548.
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T57 BT4661/heparin complex. Structure of Bt4661, a Suse-Like Surface Located Polysaccharide Binding Protein from the Bacteroides Thetaiotaomicron Heparin Utilisation Locus. EC Lowe, A Basle, M Czjzek, S Thomas, H Murray, SJ Firbank, DN Bolam, D.N. ? ?4AK2 ? ?
T58 PliG /SalG lysozyme complex with SAXS data, by S. Leysen and S. Strelkov (Catholic University Leuven, Belgium) ? ?4G9S Leysen et al. (2013)
Structural basis of bacterial defense against g-type lysozyme-based innate immunity.
Cell. Mol. Life. Sci.70:1113-1122.
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