Submission rules for all types of groups
- Predictions in CASP_Commons may be submitted in 2 formats:
TS # Atomic coordinates
QA # Model accuracy assessment
- One team may make a prediction of a target by submitting up to five models
in the TS categories, and two models in the
QA category (see the QA format section for the timeline example
of a typical QA prediction).
- Each submission file should contain prediction for only one target.
- Each submission file should contain only one of the allowed format categories.
- Submission files in RR and QA categories should contain only one model.
- Submission files in TS category may contain either one or several
models. Each model should
begin with the MODEL record, end with the END record, and contain no target
residue repetitions. You may specify only one set of required header fields
(PFRMAT, TARGET, AUTHOR, METHOD) above the first MODEL record in the prediction
file. A multiple-model file will be split into separate files (one model per
file) and each model (up to 5) will be sent separately to the verification server.
- Submission of a duplicate model (same target, format category, group, model
index) will replace previously accepted model, provided it is received before
the deadline.
- Each submission must begin with the PFRMAT, TARGET and AUTHOR records,
contain the METHOD field and at least one block starting with the MODEL
and ending with the END record.
- Each submitted model is automatically verified by the format verification
server. In case of successful submission no confirmation email will be sent.
A unique model ACCESSION CODE is composed from the number of the target, prediction
format category, prediction group number, and model index.
Example:
Accession code C0001TS005_2 has the following components:
C0001 target number
TS Tertiary Structure (PFRMAT TS)
005 prediction group 5
2 model index 2
The accepted predictions could be viewed using Model Viewer link from the CASP_Commons
web page.
If the submission contains an error, the regular group leader or server contact
person will be immediately notified through email. If your prediction is rejected
for format inconsistency, you will have the possibility to correct problems and
re-send prediction(s) within the target prediction time window.
Submission rules for expert groups (usually, 3-week deadline in TS category,
3 day deadline for QA)
-
Predictions can be submitted by a group leader or a group member with submission
privileges. The group leader can set the privileges (regular member or submitter)
for every member of his group using the 'Review member status' option from
'My CASP_Commons profile' link. Members of prediction groups who intend to submit predictions
should receive submission permission from the group leader first and then use
the 12-digit Registration Code of the group to submit predictions for that group.
- Models for regular deadline groups should be submitted directly by e-mail to
models AT predictioncenter.org or using
the CASP_Commons model submission facility.
-
When sending predictions by email, please send them in the body of the message.
-
When sending predictions by email, please remember to use
only the email address registered with the Prediction Center
as origination points (make sure we have
the updated email address for you on file - check for this your "My Personal Data"
link from the menu). If you temporary cannot use the registered email address for
submission, please use the submission form
instead.
-
Time for returning regular group predictions is set separately for each target.
Usually regular deadline predictors have around 3 weeks
from the date of target release to return a prediction.
-
Predictions in TS categories should contain sensible residue error estimates
(in Angstroms) in the column reserved for the B-factor value in the PDB format.
Submission rules for server groups (3-day deadline)
-
CASP_Commons queries will NOT be sent to the registered servers from the CASP distribution
server. Please submit queries to your server yourself and make sure that we receive
your predictions at models AT predictioncenter.org by the server prediction deadline.
TS servers are requested to return predictions in 5 days from the target release time.
No additional time for corrections will be allotted, but corrections will be accepted
within the original prediction window. Please, send your corrections manually to the
address specified in the REPLY-E-MAIL field of the original query. Remember, that
corrections can be submitted only by a group leader or a group member with submission
privileges. The group leader can set the privileges (regular member or submitter)
for every member of his group using the 'Review member status' option from
'My CASP_Commons profile' link. Members of prediction groups who intend to submit predictions
should receive submission permission from the group leader first.
-
Server models must be submitted in the body of the email as a plain text.
Subject of the email preferrably should contain the target number and the group name.
- Each submission may contain several models. If server returns more than 5
models, the models numbered 6 and higher will be ignored.
In the QA category please designate your model as MODEL 2.
Format description
All submissions should contain records described below.
Each of these records must begin with a standard keyword.
In all submissions standard keywords must
begin in the first column of a record.
The keyword set is as follows:
PFRMAT Format specification code: TS , QA
TARGET Target identifier from the CASP_Commons target table
AUTHOR XXXX-XXXX-XXXX Registration code of the Group Leader or Server Group Name
SCORE Reliability of the model (optional)
REMARK Comment record (may appear anywhere after the first 3 required lines, optional)
METHOD Records describing the methods used
MODEL Beginning of the data section for the submitted model
PARENT Specifies structure template used to generate the TS model
TER Terminates chain in the oligomeric TS model
END End of the submitted model
Models should be submitted in Plain Text format.
Record PFRMAT should appear on the first line of the prediction and
is used for all submissions.
PFRMAT TS
TS indicates that submission contains 3D atomic coordinates
in standard PDB format
PFRMAT QA
QA indicates that submission contains estimates of model accuracy
Record TARGET should appear on the second line of the prediction and
is used for all submissions.
TARGET Txxxx
Txxxx indicates id of the target predicted.
Record AUTHOR should appear on the third line of the prediction
and is used for all submissions.
For all groups:
AUTHOR XXXX-XXXX-XXXX
XXXX-XXXX-XXXX indicates the Group Registration code.
This is the code obtained by the group leader upon registration.
Note: Members of prediction groups who intend to submit predictions
should receive submission permissions from the group leader and
use the registration code of the Group for all predictions submitted by
that group. If sending predictions by email, please send them from the
registered emails of the group leader or group submitter.
If you temporary can not use these emails for submission, please login
to our website and then use our web-based submission facility.
Servers alternatively can be identified using their registered group names:
AUTHOR MY_SERVER_NAME
or
REMARK AUTHOR MY_SERVER_NAME
where MY_SERVER_NAME is a name selected for the server group at registration
SCORE Optional. This record may be used to report a model
reliability score. It will not influence the evaluation.
REMARK Optional. PDB style 'REMARK' records may be used
anywhere in the submission. These records may contain any
text and will in general not influence evaluation.
Records METHOD are used for all submissions.
These records describe the method used. Predictors are urged to provide
a concise description of the method, including data libraries used,
and values of default and non-default parameters.
Record MODEL is used for all submissions.
Signifies the beginning of model data.
MODEL n
n Model index n is used to indicate predictor's ranking
according to her/his belief which TS model is closest to the
target structure (1 <= n <= 5). Model index is included
automatically in the ACCESSION CODE. All models with index
higher than 5 will be discarded.
In QA category, predictors are requested to use model index '2' for all submissions.
Record PARENT is required only for the submissions in the TS format.
PARENT record indicates structure templates used to generate the MODEL
(see description of the TS format below).
One PARENT record is required for every prediction.
PARENT N/A
Indicates that a prediction is not directly based on any known
structure. Note that this is the only indication in the file that the
prediction is ab initio, so is a critical piece of information.
PARENT 1abc_A
Indicates that the model is
based on a single PDB entry 1abc chain A (use _A to indicate chain A).
All template-based predictions should be submitted with this form
of the PARENT record. Note that, in order to be accepted, the code
must correspond to a current PDB entry.
PARENT 1cdc 2def_g [3hij_k ...]
Indicates that the model is based on more than one structural template.
Up to five PDB chains may be listed here with additional detailed information
included in the METHOD records.
Record TER is used to terminate chains in TS predictions.
TER
Atomic coordinates (PFRMAT TS).
Standard PDB atom records are used for the atomic coordinates. Format of the
submission requires that 80 column long records are used. These may be spaces
when needed (see target template PDB files as provided in specific target
descriptions available through the CASP_Commons target table).
Coordinate section for each model should begin
with a single PARENT record and terminate with a TER record.
It is requested that coordinate data be supplied for at least all
non-hydrogen main chain atoms, i.e. the N, CA, C and O atoms of every residue.
For any given MODEL, no target residue may be repeated in the prediction.
For quaternary structure predictions, coordinates for all chains should be submitted
in the same frame of reference. Chains should be labeled 'A', 'B', ... according
to the provided template for each target.
Atoms for which a prediction has been made must contain a value between 0.01 and 1.00
(usually "1.00") in the occupancy field; those for which no prediction has been
made must either contain "0.00" in that field or be skipped altogether.
In place of temperature factor field, the error estimates, in Angstroms, should
be provided. We require all predictors to submit the error estimates as these
will be used in the evaluation. Models with all residues having the same 'B-factor'
will be rejected. If your software predicts per-residue B-factor-like score
instead of distance in Angstroms - please convert your B-score to distance d
inverting the formula B=(8pi^2*d^2)/3 (or indicate nature of your score
in the REMARKS).
Estimation of model accuracy (PFRMAT QA).
In QA category, predictors are requested to use model index '2' for all submissions.
Data are inserted between MODEL and END records of the submission file.
You may submit your quality assessment prediction in one of the two different modes:
QMODE 1 : global model quality score (MQS - one number per model)
QMODE 2 : MQS and error estimates on per-residue basis.
The first line of data should specify mode identifier, i.e. QMODE (see Example 3).
In both modes, the first column in each line contains model identifier (file name of the
accepted 3D prediction).
The second column contains the accuracy score for a model as a whole (MQS).
The accuracy score is a real number between 0.0 and 1.0 (1.0 being a perfect model).
If you don't provide MQS for a model please put "X" in the corresponding place.
If you don't want to additionally provide error estimates on per residue basis
(QMODE 1), your data table will consist of these two columns only.
If you do additionally provide residue error estimates (QMODE 2),
each consecutive column should contain error estimate in Angstroms for all the
consecutive resides in the target (i.e., column 3 corresponds to residue 1 in
the target, column 4 - to residue 2 and so on). This way data constitute a table
(Number_of_models_for_the_target) BY (Number_of_residues_in_the_target + 1).
Do not skip columns if you are not predicting error estimates for some residues -
instead put "X" in the corresponding column.
Please specify in the REMARKS what you consider to be an error estimate for a residue
(CA location error, geometrical center error, etc.).
Note 1.
Please, be advised that a QA record line may be very long and that some
editors/mailing programs may force line wrap potentially causing unexpected parsing errors.
To avoid this problem we recommend that you split long lines into shorter sublines
(50-100 columns of data) by yourself. Our parser will consider consecutive sublines
(starting with the line containing evaluated model name and ending with the line
containing the next model name or tag END) a part of the same logical line.
Note 2.
Please, be advised that model quality predictions in CASP are evaluated
by comparing submitted estimates of global reliability and
per-residue accuracy of structural models with the values obtained from
CASP model evaluation packages (LGA, LDDT, CAD-score and others). Since
the evaluation score that is used across the categories in CASP is GDT_TS,
predictors should strive to predict this score in QMODE1 (QA1).
Predicted per-residue distances in QMODE2 should ideally reproduce those
extracted from the LGA optimal model-target superpositions.
END record is used for all predictions and indicates the end of a
single model submission.
Example 1. Atomic coordinates (Tertiary Structure)
The primary CASP_Commons format used for tertiary structure prediction
PFRMAT TS
TARGET C0001
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT 1abc 1def_A
ATOM 1 N GLU 1 10.982 -9.774 1.377 1.00 0.50
ATOM 2 CA GLU 1 9.623 -9.833 1.984 1.00 0.50
ATOM 3 C GLU 1 8.913 -11.104 1.521 1.00 0.50
ATOM 4 O GLU 1 9.187 -11.630 0.461 1.00 0.50
ATOM 5 CB GLU 1 8.814 -8.614 1.546 1.00 0.50
ATOM 6 CG GLU 1 7.372 -8.754 2.039 1.00 0.50
ATOM 7 CD GLU 1 7.339 -8.625 3.562 1.00 0.50
ATOM 8 OE1 GLU 1 8.370 -8.307 4.131 1.00 0.50
ATOM 9 OE2 GLU 1 6.284 -8.846 4.132 1.00 0.50
ATOM 10 N THR 2 7.998 -11.599 2.304 1.00 1.60
ATOM 11 CA THR 2 7.266 -12.832 1.907 1.00 1.60
ATOM 12 C THR 2 6.096 -12.456 1.005 1.00 1.60
ATOM 13 O THR 2 5.008 -12.217 1.466 1.00 1.60
ATOM 14 CB THR 2 6.731 -13.533 3.157 1.00 1.60
ATOM 15 OG1 THR 2 7.662 -13.379 4.220 1.00 1.60
ATOM 16 CG2 THR 2 6.526 -15.019 2.864 1.00 1.60
ATOM 17 N VAL 3 6.308 -12.396 -0.278 1.00 1.70
ATOM 18 CA VAL 3 5.190 -12.030 -1.187 1.00 1.70
ATOM 19 C VAL 3 3.954 -12.870 -0.844 1.00 1.70
ATOM 20 O VAL 3 2.834 -12.471 -1.090 1.00 1.70
ATOM 21 CB VAL 3 5.608 -12.274 -2.641 1.00 1.70
ATOM 22 CG1 VAL 3 5.542 -13.771 -2.959 1.00 1.70
ATOM 23 CG2 VAL 3 4.664 -11.514 -3.573 1.00 1.70
ATOM 24 N GLU 4 4.146 -14.029 -0.272 1.00 1.70
ATOM 25 CA GLU 4 2.976 -14.882 0.086 1.00 1.60
ATOM 26 C GLU 4 2.153 -14.190 1.175 1.00 1.50
ATOM 27 O GLU 4 0.942 -14.141 1.109 1.00 1.40
ATOM 28 CB GLU 4 3.465 -16.238 0.597 1.00 1.30
ATOM 29 CG GLU 4 2.336 -17.264 0.479 1.00 1.20
ATOM 30 CD GLU 4 2.929 -18.671 0.391 1.00 1.10
ATOM 31 OE1 GLU 4 4.056 -18.846 0.823 1.00 1.00
ATOM 32 OE2 GLU 4 2.246 -19.551 -0.108 1.00 0.90
TER
END
Example 2. Multichain predictions
PFRMAT TS
TARGET C0001
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
PARENT N/A
ATOM 1 N GLU A 1 22.576 19.032 -5.026 1.00 0.00
ATOM 2 CA GLU A 1 22.879 20.313 -4.321 1.00 0.00
ATOM 3 CB GLU A 1 22.285 21.478 -5.449 1.00 0.00
ATOM 4 CG GLU A 1 23.018 21.946 -6.707 1.00 0.00
ATOM 5 CD GLU A 1 24.351 22.625 -6.434 1.00 0.00
ATOM 6 OE1 GLU A 1 25.379 21.908 -6.380 1.00 0.00
ATOM 7 OE2 GLU A 1 24.381 23.879 -6.291 1.00 0.00
ATOM 8 O GLU A 1 22.237 20.962 -2.117 1.00 0.00
ATOM 9 C GLU A 1 21.857 20.684 -3.261 1.00 0.00
ATOM 10 N VAL A 2 20.585 20.675 -3.601 1.00 0.00
ATOM 11 CA VAL A 2 19.530 21.006 -2.624 1.00 0.00
ATOM 12 CB VAL A 2 18.277 21.590 -3.319 1.00 0.00
ATOM 13 CG1 VAL A 2 17.182 21.859 -2.270 1.00 0.00
ATOM 14 CG2 VAL A 2 18.656 22.833 -4.079 1.00 0.00
ATOM 15 O VAL A 2 18.770 18.750 -2.603 1.00 0.00
ATOM 16 C VAL A 2 19.096 19.721 -1.933 1.00 0.00
ATOM 17 N HIS A 3 19.115 19.700 -0.603 1.00 0.00
ATOM 18 CA HIS A 3 18.780 18.489 0.122 1.00 0.00
ATOM 19 CB HIS A 3 19.559 18.445 1.410 1.00 0.00
ATOM 20 CG HIS A 3 21.015 18.684 1.224 1.00 0.00
ATOM 21 CD2 HIS A 3 21.767 19.803 1.367 1.00 0.00
ATOM 22 ND1 HIS A 3 21.851 17.721 0.702 1.00 0.00
ATOM 23 CE1 HIS A 3 23.072 18.220 0.589 1.00 0.00
ATOM 24 NE2 HIS A 3 23.048 19.478 0.985 1.00 0.00
ATOM 25 O HIS A 3 16.777 19.181 1.220 1.00 0.00
ATOM 26 C HIS A 3 17.296 18.417 0.409 1.00 0.00
TER
PARENT 1abc
ATOM 1321 N GLU B 1 -22.603 -17.981 -4.847 1.00 0.00
ATOM 1322 CA GLU B 1 -22.889 -19.285 -4.180 1.00 0.00
ATOM 1323 CB GLU B 1 -22.342 -20.410 -5.372 1.00 0.00
ATOM 1324 CG GLU B 1 -23.122 -20.828 -6.619 1.00 0.00
ATOM 1325 CD GLU B 1 -24.447 -21.511 -6.324 1.00 0.00
ATOM 1326 OE1 GLU B 1 -25.468 -20.792 -6.207 1.00 0.00
ATOM 1327 OE2 GLU B 1 -24.479 -22.769 -6.227 1.00 0.00
ATOM 1328 O GLU B 1 -22.172 -20.020 -2.026 1.00 0.00
ATOM 1329 C GLU B 1 -21.830 -19.701 -3.172 1.00 0.00
ATOM 1330 N VAL B 2 -20.572 -19.685 -3.557 1.00 0.00
ATOM 1331 CA VAL B 2 -19.485 -20.056 -2.630 1.00 0.00
ATOM 1332 CB VAL B 2 -18.260 -20.619 -3.392 1.00 0.00
ATOM 1333 CG1 VAL B 2 -17.131 -20.932 -2.393 1.00 0.00
ATOM 1334 CG2 VAL B 2 -18.674 -21.832 -4.184 1.00 0.00
ATOM 1335 O VAL B 2 -18.711 -17.807 -2.553 1.00 0.00
ATOM 1336 C VAL B 2 -19.020 -18.800 -1.909 1.00 0.00
ATOM 1337 N HIS B 3 -18.990 -18.829 -0.580 1.00 0.00
ATOM 1338 CA HIS B 3 -18.623 -17.648 0.178 1.00 0.00
ATOM 1339 CB HIS B 3 -19.356 -17.649 1.494 1.00 0.00
ATOM 1340 CG HIS B 3 -20.819 -17.875 1.353 1.00 0.00
ATOM 1341 CD2 HIS B 3 -21.571 -18.995 1.480 1.00 0.00
ATOM 1342 ND1 HIS B 3 -21.667 -16.890 0.896 1.00 0.00
ATOM 1343 CE1 HIS B 3 -22.894 -17.378 0.809 1.00 0.00
ATOM 1344 NE2 HIS B 3 -22.864 -18.650 1.156 1.00 0.00
ATOM 1345 O HIS B 3 -16.586 -18.389 1.177 1.00 0.00
ATOM 1346 C HIS B 3 -17.129 -17.592 0.414 1.00 0.00
TER
END
Example 3. Estimates of model accuracy prediction
(A) Global Model Quality Score
PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
METHOD Description of methods used
MODEL 2
QMODE 1
C1901TS001_1 0.8
C1901TS003_1 0.4
C1901TS005_1 0.2
END
(B) Residue-based Quality Assessment (fragment of the table). Note, that this case includes case (A) and there is no need to submit QMODE 1 predictions additionlly to QMODE 2.
PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Residue's error estimate is the CA-CA distance in Angstroms in the optimal model-target superposition
METHOD Description of methods used
MODEL 2
QMODE 2
C1901TS001_1 0.8 10.0 6.5 5.0 2.0 1.0
5.0 4.3 4.6 ...
C1901TS003_1 0.7 8.0 5.5 4.5 X X
4.5 4.2 5.0 ...
END
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