CAPRI: Critical Assessment of PRediction of Interactions

Result (Target 122)

For T122, the sequence ID threshold was lowered to 30%, since a significant fraction of participants only modeled part of the system. Since this was the interaction part, it made sense to modify the scoring criteria and not disqualify those submissions.

Results are good, with 2 medium-quality and 7 acceptable submissions in top-1, these numbers increasing to 4 and 24 for top-5.

                    Predictor top            Scorer top
                    1    3    5   10  100    1    3    5   10 
  high              0    0    0    0    0    0    0    0    0 
  medium            2    4    4    7    7    0    1    1    5 
  acceptable        7   16   24   39  107    4    9   15   20 
  incorrect        24   76  133  274 1967   16   49   82  173 
  clashes/lowid     2    5    6   11  300    0    1    2    2 
  total            35  103  171  339 2389   20   60  100  200 

Result (Target 123)

T123 was the binding of PorM N-terminal domain with a nanobody. the PorM was not provided as unbound, but there are hundreds of hits for nanobodies, including the appropriate one (released by the PDB at the beginning of the prediction round).

This was a difficult target; the whole set of submissions contained *one* acceptable model.

Summary for T123:

                    Predictor top            Scorer top
                    1    3    5   10  100    1    3    5   10 
  high              0    0    0    0    0    0    0    0    0 
  medium            0    0    0    0    0    0    0    0    0 
  acceptable        0    0    0    0    1    0    0    0    0 
  incorrect        29   85  145  290 1902   15   49   82  174 
  clashes/lowid     2    8    9   19  484    4    8   13   16 
  total            32   96  160  320 2403   19   57   95  190 

Result (Target 124)

T124 was the binding of the PorM C-terminal domain, as dimer, to a nanobody. the PorM dimer was not provided (released by PDB 6 months after the prediction round) and basically had no templates. the structure of the nanobody was released by the PDB at the start of the prediction round.

Assessment T124.1 is the dimeric PorM interface, of 2000 A2.
Assessment T124.2 is the interface between a PorM monomer and the camelid antibody.

No acceptable submissions.

Summary for T124.1:

                    Predictor top            Scorer top
                    1    3    5   10  100    1    3    5   10 
  high              0    0    0    0    0    0    0    0    0 
  medium            0    0    0    0    0    0    0    0    0 
  acceptable        0    0    0    0    0    0    0    0    0 
  incorrect        29   87  145  290 1966    9   27   45   86 
  clashes/lowid     0    0    0    0   90    0    0    0    0 
  total            29   87  145  290 2056    9   27   45   86 

Summary for T124.2:

                    Predictor top            Scorer top
                    1    3    5   10  100    1    3    5   10 
  high              0    0    0    0    0    0    0    0    0 
  medium            0    0    0    0    0    0    0    0    0 
  acceptable        0    0    0    0    0    0    0    0    0 
  incorrect        26   82  137  279 1802   17   48   84  171 
  clashes/lowid     2    2    4    5  112    1    2    2    3 
  total            29   87  145  290 2056   18   54   90  180 

Link to result details:
Result details for T124.1
Result details for T124.2

ID mappings

Announcement

This Round offers a total of 3 targets: T122, T123, T124.

T122 is a human cytokine receptor complex: (IL23-IL23R), structure determined at 2.8Å, offered by Savvas Savvides, Dept. Bochemistry & Microbiology, Ghent University, Belgium.

T123, T124 are two high-resolution complexes of the Nter and Cter domains respectively, of PorM, a component of the bacterial type 9 secretion system, with a camelid nanobody. The targets are offered by Alain Roussel, Université Aix Marseille.

Please note that we are now asking predictors to submit up to 100 models directly to the EBI CAPRI website at the date of the predictor submission deadline. For targets where template-based modeling/docking is used, predictors are highly encouraged to submit as many models as possible.

Therefore, the step of separately uploading models for the scoring challenge to the CNRS/Lille website is eliminated.

Note also, that the first 10 models of the submitted set will be considered as the 10 best models to be evaluated as predictor models have been in the past, except that from now on the model ranking will be evaluated as well.

As previously, the (larger) set of submitted models will be used to generate the datasets for scoring challenge. Those will still be made available from the CNRS/Lille site for this scoring Round. The CNRS/Lille site is also where the scoring submission has to be deposited.

Documentation and Targets Round 39

• April 10 - registration begins

• April 18 - prediction Round opens
• April 21 - deadline for server submissions
• May 21 - deadline for submitting predictions
• May 26 - scoring Round set available
• May 31 - scoring Round submission deadline

• Download Target information
• Upload Opens April 18 2017

• Participants
• Management Group
• Prediction formats

SCORERS

Scorers can download the server set of submissions from
https://cb.iri.univ-lille1.fr/capri/ using the same login user/pass as distributed for Capri round39. Full details and deadlines are given on this site.

Email Problems or Queries to Sameer Velankar