- Models should be submitted via the web upload service.
- 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.
Example
If the following is met for format then we can automatically
process the submissions with ease:
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