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CAPRI: Critical Assessment of PRediction of Interactions
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 MSD  CAPRI: Critical Assessment of PRediction of Interactions

Third community wide experiment on the comparative evaluation of protein-protein docking for structure prediction

Hosted By EMBL/EBI-MSD Group


Please use these files for standard chain Identifiers
PLEASE NOTE: For submissions only files uploaded that conform to the format defined in the starting files and described in the format document will be accepted as valid submissions. The submission procedure will automatically reject files that fail format checking.

Targets 08: Nidogen-G3/laminin (unbound/bound)

T08 is from Pr. Timothy A. Springer (Harvard Medical School)
Nidogen-G3 domain (bound) in complex with three laminin EGF-like modules 1KLO (Stetefeld et al., 1996, JMB 257:644) Nidogen-G3 is known to bind mostly, but not necessarily exclusively, to the middle domain (residues 65-120) of the laminin fragment. We suggest docking nidogen-G3 on the whole fragment and on the middle domain separately. However, only ten solutions will be permitted in total.
NOTE: For target 08 there has been a query about what to submit - does one submit coordinates for all three domains of laminin docked to nidogen or just he middle domain? The management committee has after consulting with Shoshana, decided on the simplest path, i.e. models obtained by docking on one laminin modules will contain only that module; models obtained by docking on three modules will contain all three. They should still be ranked and go into a single file. During the assessment procedure this will be taken into account in a manner as yet to be decided.

  • CAPRI3-08 Nidogen-G3/laminin EGF

    Target T09: Wild type LicT homodimer (unbound/unbound)

    Target 9 Published: see:
    J Biol Chem. 2005 Feb 7; [Epub ahead of print]
    Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes.
    Graille M, Zhou CZ, Receveur-Brechot V, Colinet B, Declerck N, van Tilbeurgh H.

    T09 is from Pr. Herman van Tilbeurgh (Orsay)
    Aim: Reconstruct the wild type LicT homodimer The structure of the H207D/H269D mutant has been published (van Tilbeurgh et al., 2001, EMBO J 20:3789) but it forms a different dimer. Use the 1H99 file after mutating Asp207 and Asp269 back to His. Ten (ranked) solutions can be submitted. T09 is wild-type LicT, with the same two domains as in 1H99 and no phosphorylation. Download

  • CAPRI3-09 wild type LicT homodimer