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CAPRI: Critical Assessment of PRediction of Interactions

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

Hosted By EMBL/EBI-PDBe Group

Formats for Prediction Submission

This document describes the format required for submissions of CAPRI predictions.

General rules

  • Models should be submitted by a web upload service to Submissions

  • Predictions for CAPRI may be submitted only in the PDB format:

  • The submission must have the CAPRI-target number in the first line as a HEADER record.

  • One team may make a prediction of a target by submitting up to 10 models in the PDB format in a manner to taht used for NMR ensembles, i.e. separated by MODEL and ENDMDL keywords. Chains should end with a TER keyword.

  • AUTHOR's should be in the PDB format

  • PDB COMPND records should describe the CHAIN assignments used for the different proteins

  • Each entry of 1 or models must terminate with an END record

  • Any annotation on methods can be put in unformatted REMARK records

  • coordinates are to submitted as standard PDB ATOM/HETATM records

  • Each submitted model will be processed by EBI deposition annotation software.

If the following is met for format then we can automatically process the submissions with ease.#

Example

HEADER    CAPRI_02
COMPND    MOL_ID: 1;  
COMPND   2 MOLECULE: VIRAL CAPSID VP6; 
COMPND   3 CHAIN: A, B, C;
COMPND   4 MOL_ID: 2;
COMPND   5 MOLECULE: FAB, KAPPA LIGHT CHAIN;
COMPND   6 CHAIN: L;
COMPND   7 MOL_ID: 3;
COMPND   8 CHAIN H;
COMPND   9 MOLECULE: FAB, IG HEAVY CHAIN 
EXPDTA    THEORETICAL MODEL,1 STRUCTURES
AUTHOR    submittor
REMARK     Predictor remarks

CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1 
SCALE1 1.000000  0.000000  0.000000   0.00000 
SCALE2 0.000000  1.000000  0.000000   0.00000 
SCALE3 0.000000  0.000000  1.000000   0.00000 
MODEL        1
ATOM      4  N   MET A   1 23.616  -6.024   3.029  1.00 20.67
ATOM      5  CA  MET A   1 23.057  -4.914   3.794  1.00 20.80
(...)
ATOM   3175  NZ  LYS A 397 13.121   4.639  20.328  1.00 50.11
ATOM   3176  OXT LYS A 397 17.870   0.132  22.866  1.00 50.72
TER    3177          A 397
ATOM   3181  N   MET B   1  3.029  23.616  -6.024  1.00 20.67
(...)
ATOM   6352  NZ  LYS B 397 20.328  13.121   4.639  1.00 50.11
ATOM   6353  OXT LYS B 397 22.866  17.870   0.132  1.00 50.72
TER    6354      LYS B 397
ATOM   6358  N   MET C   1 -6.024   3.029  23.616  1.00 20.67
ATOM   6359  CA  MET C   1 -4.914   3.794  23.057  1.00 20.80
(...)
ATOM   9529  NZ  LYS C 397  4.639  20.328  13.121  1.00 50.11
ATOM   9530  OXT LYS C 397  0.132  22.866  17.870  1.00 50.72
TER    9531      LYS C 397
ATOM      1  CB  ASP L   1 -5.859  28.852  76.956  1.00 55.84
ATOM      2  CG  ASP L   1 -6.496  29.295  75.685  1.00 55.84
(...)
ATOM   1637  O   ARG L 211     -40.305 -17.023  48.625  1.00 66.48
ATOM   1638  OT  ARG L 211     -41.130 -14.944  48.552  1.00 60.71
TER              ARG L 211
ATOM   1639  CB  GLU H   0  3.480  -2.102  95.482  1.00 95.00
ATOM   3236  O   GLU H 208     -30.889 -26.738  60.340  1.00 61.67
ATOM   3237  OT  GLU H 208     -31.330 -25.575  58.484  1.00 67.04
TER              GLU H 208
ENDMDL
MODEL        2
(...)
ENDMDL
END
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