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CAPRI: Critical Assessment of PRediction of Interactions

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

Hosted By EMBL/EBI-MSD Group

Round 23

Round 23 ID mapping from group number to Accessor Number for Target 47
Round 23 ID mapping from group number to Accessor Number for Target 48
Round 23 ID mapping from group number to Accessor Number for Target 49
NOTE The Coordinates are not yet available for download

T47 result summary
T48 result summary
T49 result summary

Target 47

 Results T47 - click here to see the results

T47 required no docking; templates 1emv and 2wpt were 3-star models, with L-rms of 1.30 and 1.49 A, and I-rms of 0.83 and 0.72 A, resp. These were trivial solutions, that everyone should've had.

Indeed, the prediction of position of water molecules was the true challenge in this target. The water assessment is explained in the document here


Full results (regular assessment):
Clash threshold78.60
average22.47
std dev28.07
PredictorUploaderScorer
Nr groups291214
High Accuracy (***)95 (20)278 ( 9)63 (12 <- 7)
Medium (**)108 (19)305 ( 8)38 (10 <- 4)
Acceptable (*)13 ( 7)20 ( 5)0 ( 0 <- 0)
Incorrect47 ( 9)391 ( 6)22 ( 6 <- 6)
Clashes14 ( 3)57 ( 2)5 ( 2 <- 1)
Low Id0 ( 0)0 ( 0)0 ( 0 <- 0)
Total277 (29)1051 (11)128 (13 <- 11)

Numbers in parentheses refer to the number of different source groups producing these models (ie z scorer groups recognize y out of x uploader groups)


Full results (water assessment):
PredictorUploaderScorer
Nr groups291214
Outstanding (****)0 ( 0)0 ( 0)0 ( 0 <- 0)
Excellent (***)11 ( 3)43 ( 3)5 ( 2 <- 1)
Good (**)60 (14)174 ( 5)36 (10 <- 5)
Fair (*)75 (16)152 ( 5)29 ( 9 <- 3)
Bad114 (18)682 ( 8)58 (10 <- 9)
Clashes17 ( 2)0 ( 0)0 ( 0 <- 0)
Total277 (29)1051 (11)128 (13 <- 11)

Individual values for fw_nat and fw_nonnat can be found in this document

Target 48

 Results T48 - click here to see the results

Results T48 (trimer)- click here to see the results

Binding of a hydroxylase and ferredoxin. The hydroxylase is a hetero-hexamer and has two binding sites for ferredoxin, but participants were invited to submit only solutions that involve the first ABC trimer. There was some confusion among the participants on whether to use the trimer or the hexamer for docking. Well, the ferredoxin binds to one chain of one trimer but also to a different chain of the other trimer. In addition, the hydroxylase exists as a hetero-hexamer and that is the entity to which ferredoxin binds.


The scoring experiment for T48 was included in T49.


Full results:

Clash threshold110.61
average30.40
std dev40.10

PredictorUploaderScorer
Nr groups20110
High Accuracy (***)0 ( 0)0 ( 0)0 ( 0 <- 0)
Medium (**)4 ( 2)6 ( 4)0 ( 0 <- 0)
Acceptable (*)17 ( 7)43 ( 6)0 ( 0 <- 0)
Incorrect116 (16)779 ( 9)0 ( 0 <- 0)
Clashes21 ( 4)18 ( 2)0 ( 0 <- 0)
Low ID0 ( 0)0 ( 0)0 ( 0 <- 0)
Total158 (16)846 ( 9)0 ( 0 <- 0)

Since so many participants submitted solutions involving the trimer, we've also assessed those prediction:

Clash threshold86.46
average22.19
std dev32.14

PredictorUploaderScorer
Nr groups32140
High Accuracy (***)0 ( 0)2 ( 1)0 ( 0 <- 0)
Medium (**)11 ( 6)12 ( 6)0 ( 0 <- 0)
Acceptable (*)39 (14)76 ( 9)0 ( 0 <- 0)
Incorrect237 (31)1246 (14)0 ( 0 <- 0)
Clashes21 ( 5)10 ( 4)0 ( 0 <- 0)
Low ID0 ( 0)0 ( 0)0 ( 0 <- 0)
Total308 (31)1346 (14)0 ( 0 <- 0)

Target 49

 Results T49 - click here to see the results

Results T49 (trimer)- click here to see the results

Same target as T48, different hexamer conformation.


Full results:

Clash threshold132.68
average41.69
std dev45.50

PredictorUploaderScorer
Nr groups181111
High Accuracy (***)0 ( 0)0 ( 0)0 ( 0 <- 0)
Medium (**)1 ( 1)3 ( 1)1 ( 1 <- 1)
Acceptable (*)11 ( 7)45 ( 7)4 ( 3 <- 2)
Incorrect123 (16)787 ( 9)71 (10 <- 7)
Clashes23 ( 5)15 ( 1)0 ( 0 <- 0)
Low ID0 ( 0)0 ( 0)0 ( 0 <- 0)
Total158 (16)850 ( 9)76 (10 <- 7)

Numbers in parentheses refer to the number of different source groups producing these models (ie z scorer groups recognize y out of x uploader groups)


Assessment against the trimer:

Clash threshold69.54
average20.90
std dev24.32

PredictorUploaderScorer
Nr groups331413
High Accuracy (***)0 ( 0)6 ( 3)0 ( 0 <- 0)
Medium (**)1 ( 1)10 ( 6)1 ( 1 <- 1)
Acceptable (*)35 (14)87 (10)19 ( 7 <- 5)
Incorrect247 (30)1193 (14)90 (11 <- 11)
Clashes25 ( 5)54 ( 3)0 ( 0 <- 0)
Low ID0 ( 0)0 ( 0)0 ( 0 <- 0)
Total308 (31)1350 (14)110 (11 <- 11)


ROUND 23 Timeline
30th Aug 2010 - Registration opens for Round 23
13th Sep 2010 - Round 23 opens - Prediction of Targets 47, 48 and 49
3rd Oct 2010 - Deadline for submitting models of T47, T48 and T49
7th Oct 2010 - Scoring starts
10th Oct 2010 - Deadline for scoring submission

Target 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.

Target T48, 49 are the same protein-protein complex (unbound/unbound), starting from
two different unbound structures.

Documentation and Targets Round 23

  • Participants
  • Management Group
  • Prediction formats
  • Download Opens 13th September 2010
  • Upload Opens 3rd October 2010
  • Scoring download open 10th October 2010

    • Entries

  • Current submissions

    • SCORERS

    Scorers can download the server set of submissions from
    http://www.scmbb.ulb.ac.be/capri/ using the same login user/pass as distributed for Capri round23. Full details and deadlines are given on this site.

    Email Problems or Queries to Sameer Velankar

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