Submission rules for all types of groups
- Predictions in CASP13 may be submitted in 4 formats:
TS # Atomic coordinates (tertiary or quaternary structure)
RR # Pairs of residues in contact
QA # Model accuracy assessment
- One team may make a prediction of a target by submitting up to five models
in the TS categories, one model in the RR category and two models in the
QA category (see the QA format section for the timeline example
of a typical QA prediction).
- Submissions for regular prediction targets, assembly targets, refinement targets
and data-assisted targets should be submitted in the TS format.
- 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 categories may contain either one or several
models. Most of the evaluation and assessment will focus on
the model labeled '1' (model index 1, see MODEL record). 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 T0444TS005_2 has the following components:
T0044 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 CASP13
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 and RR categories, 2 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 CASP13 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 CASP13 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 and RR categories should be normally sent only on all-group targets.
-
Predictions in TS categories should contain sensible residue error estimates in the column reserved for the B-factor value in the PDB format.
-
Predictions in QA category should be sent for all targets.
-
Multichain predictions should be sent for heteromeric targets (names starting with 'H') and homo-oligomeric targets (names starting with 'T' and stoichiometry parameter other than A1).
The stoichiometry information for each target will be provided in the column 'Stoichiom' in the Target List page.
Submission rules for server groups (3-day deadline in TS and RR categories, 2 day deadline for QA)
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 , RR , QA
TARGET Target identifier from the CASP13 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 a 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 RR
RR indicates that submission contains a residue-residue
separation distance prediction
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.
Model index should be set to 1 in RR category.
In QA category, predictors are requested to use model index '1' for the predictions
submitted at the first QA stage (i.e., for the quality estimates made on the selected
set of server models released 5 days after the target release for tertiary structure
prediction), and use model index '2' for the predictions submitted on a larger set of
TS models at the second QA stage (i.e., for the quality estimates made on the models
released 2 days after the release of the first set of models in QA category).
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 monomeric prediction,
every homo-multimeric model (should be placed within the first chain),
and every subunit (first chain of every different sequence) of
hetero-multimeric models.
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 a single PDB entry 1abc, chain A
was used as a modeling template.
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 (Example 1).
These may be spaces
when needed (see target template PDB files as provided in specific target
descriptions available through the CASP13 target table).
Coordinate section for each monomeric model, each homo-oligomeric model,
or every new (different sequence) chain of hetero-multimeric model should begin
with a single PARENT record and terminate with a TER record (see above).
If a multimer's stoichiometry composition formula displays more than one equivalent
unit, the PARENT record should be supplied within the first unit only.
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 assembly prediction (Example 2), coordinates for all chains should be submitted
in one PDB-like file. Chains should be labeled 'A', 'B', ... according
to the provided template for each target. The convention for chain order is:
alphabetical, heteromeric units (different sequences) first. For example,
for a homotrimer of heterodimers please name chains in the following order:
AB (first hetero-dimer), CD (second dimer), EF (3rd dimer).
Names of heteromeric targets will start with letter 'H', e.g. H0960,
names of all other regular targets will start from letter 'T', e.g. T1001.
Homo-multimeric predictions are encouraged for all other regular targets,
if applicable. If subunits of heteromeric targets are additionally released
as separate tertiary structure prediction targets,
there will be no need to submit monomeric predictions in addition to multimeric:
we will automatically extract coordinates of each first different chain from
the assembly prediction and save it as a tertiary structure model for the
corresponding subunit.
Information on the tentative oligomeric state of the protein (the stoichiometry formula
to the best of our knowledge at the time of target release), will be announced through
the Target List page.
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).
Residue-Residue contact prediction (PFRMAT RR).
Data in this format are inserted between MODEL and END records of the
submission file.
The prediction should start with the sequence of the predicted target
splitted (if necessary) in several rows (see Example 3).
The sequence should be followed by the list of contacts in the
five-column format:
i j d1 d2 p
Notes (see Example 3):
- indices i and j of the two residues in contact should be provided
such that i < j, i.e. only half of the contact map is supplied.
- the numbers d1 and d2 indicate the distance limits defining a contact.
In CASP, a pair of residues is defined to be in contact when
the distance between their C-beta atoms (C-alpha in case of glycine)
is less then 8 Angstroms. Therefore, typically d1=0 and d2=8.
These parameters are currently dumb and left in the format
only for the consistency with previous CASPs.
- the real number p indicates probability of the two residues being
in contact, and should be in the range 0.0 - 1.0. Values larger
than 0.5 identify the pairs of residues that are predicted to be
more likely in contact than not. In binary (two-class) evaluations,
the probability value of 0.5 will be considered as the cutoff
separating contacts from non-contacts.
Contacts in the prediction should be listed
according to the decreasing probability p. If several contacts
are assigned the same probability, for the evaluation purposes
they will be considered in the order provided in the prediction.
- any pair NOT listed is assumed to be predicted as not in contact.
- for multichain predictions, residue indices should be composed of
chain ID and residue number, e.g. A2, B44 (see Example 3B).
Estimation of model accuracy (PFRMAT QA).
In QA category, predictors are requested to use model index '1' for predictions
submitted in the first stage (i.e., estimating quality of the selected
server models released 5 days after the initial target release),
and use model index '2' for predictions submitted on the second, larger set of
TS models (i.e., estimating quality of models released 7 days after the
initial target release).
Timeline example.
May 1, 9am PDT - target T0644 is released for prediction in non-QA categories.
May 4, noon - the deadline for submitting tertiary structure predictions by servers.
May 6, noon - the first set of server TS predictions (up to 20 models selected
primarily to test single-model methods) is sent to the registered QA servers and
posted on the casp13 archive page (http://predictioncenter.org/download_area/CASP13/server_predictions/).
QA predictions (marked as MODEL 1) for this subset are accepted for two days.
May 8, noon - deadline for "stage 1" QA predictions. The second set of server TS predictions
(150 models selected to test both, single-model and clustering methods) is sent to the
registered QA servers and posted on the casp13 archive page. QA predictions
(marked as MODEL 2) for this second subset of models are accepted for two more days.
May 10, noon - deadline for "stage 2" QA predictions. All server TS predictions are posted on
the casp13 archive page. No further QA predictions (from servers or manual groups) are accepted
for this target.
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 4).
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 error estimates on per residue basis, your data table will consist
of these two columns only (Example 4A).
If you do additionally provide residue error estimates (QMODE 2),
each consecutive column should contain error estimate in Angstroms for all the
consecutive residues 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. (Example 4B)
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 CASP13 format used for tertiary structure prediction
An example of a monomeric prediction.
PFRMAT TS
TARGET T0999
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. Assembly prediction (quaternary structure)
An example of prediction for a homodimer of heterodimers.
PFRMAT TS
TARGET H0999
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 ALA A 2 66.410 61.318 7.312 1.00 2.56 N
ATOM 2 CA ALA A 2 67.149 60.105 6.984 1.00 3.55 C
ATOM 3 C ALA A 2 66.481 58.861 7.568 1.00 6.24 C
ATOM 4 O ALA A 2 66.323 57.855 6.871 1.00 2.19 O
ATOM 5 CB ALA A 2 68.602 60.207 7.448 1.00 1.18 C
ATOM 6 N ARG A 3 66.088 58.921 8.836 1.00 3.80 N
ATOM 7 CA ARG A 3 65.379 57.793 9.441 1.00 2.96 C
ATOM 8 C ARG A 3 63.851 57.931 9.360 1.00 4.56 C
ATOM 9 O ARG A 3 63.225 58.629 10.165 1.00 6.84 O
ATOM 10 CB ARG A 3 65.832 57.564 10.878 1.00 9.52 C
ATOM 11 CG ARG A 3 67.276 57.122 11.014 1.00 4.18 C
ATOM 12 CD ARG A 3 67.694 57.037 12.485 1.00 5.62 C
ATOM 13 NE ARG A 3 67.073 55.906 13.171 1.00 2.65 N
ATOM 14 CZ ARG A 3 67.192 55.663 14.473 1.00 6.45 C
ATOM 15 NH1 ARG A 3 67.898 56.480 15.241 1.00 2.61 N
ATOM 16 NH2 ARG A 3 66.596 54.608 15.011 1.00 1.01 N
ATOM 17 N ILE A 4 63.261 57.272 8.370 1.00 0.59 N
ATOM 18 CA ILE A 4 61.810 57.250 8.216 1.00 9.32 C
ATOM 19 C ILE A 4 61.262 56.084 9.014 1.00 2.36 C
ATOM 20 O ILE A 4 61.515 54.920 8.685 1.00 5.81 O
ATOM 21 CB ILE A 4 61.418 57.061 6.750 1.00 5.05 C
ATOM 22 CG1 ILE A 4 61.958 58.216 5.903 1.00 5.45 C
ATOM 23 CG2 ILE A 4 59.899 56.935 6.606 1.00 2.20 C
ATOM 24 CD1 ILE A 4 61.682 58.059 4.405 1.00 4.87 C
TER
PARENT 1abc
ATOM 577 N GLN B 1 28.350 17.252 8.838 1.00 8.30 N
ATOM 578 CA GLN B 1 28.340 18.142 7.644 1.00 6.24 C
ATOM 579 C GLN B 1 28.765 19.556 8.023 1.00 5.61 C
ATOM 580 O GLN B 1 28.866 19.893 9.209 1.00 6.62 O
ATOM 581 CB GLN B 1 26.941 18.176 7.013 1.00 6.82 C
ATOM 582 CG GLN B 1 26.851 19.045 5.768 1.00 6.64 C
ATOM 583 CD GLN B 1 26.103 18.370 4.654 1.00 8.30 C
ATOM 584 OE1 GLN B 1 26.147 17.151 4.527 1.00 1.37 O
ATOM 585 NE2 GLN B 1 25.426 19.152 3.825 1.00 8.67 N
ATOM 586 N LYS B 2 29.007 20.382 7.007 1.00 3.53 N
ATOM 587 CA LYS B 2 29.423 21.760 7.223 1.00 0.08 C
ATOM 588 C LYS B 2 28.253 22.741 7.066 1.00 7.20 C
ATOM 589 O LYS B 2 27.489 22.695 6.100 1.00 6.51 O
ATOM 590 CB LYS B 2 30.561 22.104 6.264 1.00 3.06 C
ATOM 591 CG LYS B 2 31.277 23.381 6.592 1.00 4.24 C
ATOM 592 CD LYS B 2 32.723 23.323 6.153 1.00 7.30 C
ATOM 593 CE LYS B 2 33.560 22.551 7.144 1.00 8.91 C
ATOM 594 NZ LYS B 2 34.976 23.004 7.075 1.00 0.63 N
ATOM 595 N THR B 3 28.120 23.623 8.047 1.00 3.04 N
ATOM 596 CA THR B 3 27.054 24.606 8.062 1.00 0.76 C
ATOM 597 C THR B 3 27.306 25.741 7.072 1.00 8.84 C
ATOM 598 O THR B 3 28.422 25.912 6.574 1.00 8.53 O
ATOM 599 CB THR B 3 26.897 25.215 9.469 1.00 1.71 C
ATOM 600 OG1 THR B 3 28.028 26.045 9.770 1.00 2.75 O
ATOM 601 CG2 THR B 3 26.807 24.118 10.507 1.00 8.32 C
TER
ATOM 70 N ALA C 2 17.139 38.489 7.542 1.00 4.40 N
ATOM 71 CA ALA C 2 16.401 39.708 7.233 1.00 2.49 C
ATOM 72 C ALA C 2 17.081 40.939 7.824 1.00 8.51 C
ATOM 73 O ALA C 2 17.221 41.955 7.138 1.00 2.84 O
ATOM 74 CB ALA C 2 14.954 39.610 7.712 1.00 0.41 C
ATOM 75 N ARG C 3 17.504 40.862 9.087 1.00 3.11 N
ATOM 76 CA ARG C 3 18.215 41.993 9.686 1.00 0.09 C
ATOM 77 C ARG C 3 19.746 41.845 9.588 1.00 6.10 C
ATOM 78 O ARG C 3 20.379 41.144 10.389 1.00 5.06 O
ATOM 79 CB ARG C 3 17.779 42.223 11.128 1.00 0.49 C
ATOM 80 CG ARG C 3 16.326 42.657 11.272 1.00 6.72 C
ATOM 81 CD ARG C 3 15.905 42.771 12.734 1.00 4.86 C
ATOM 82 NE ARG C 3 16.538 43.899 13.407 1.00 4.46 N
ATOM 83 CZ ARG C 3 16.460 44.127 14.712 1.00 5.48 C
ATOM 84 NH1 ARG C 3 15.783 43.294 15.485 1.00 4.75 N
ATOM 85 NH2 ARG C 3 17.057 45.186 15.239 1.00 9.68 N
ATOM 86 N ILE C 4 20.329 42.493 8.586 1.00 1.62 N
ATOM 87 CA ILE C 4 21.772 42.515 8.415 1.00 8.68 C
ATOM 88 C ILE C 4 22.324 43.671 9.214 1.00 4.12 C
ATOM 89 O ILE C 4 22.056 44.830 8.893 1.00 7.89 O
ATOM 90 CB ILE C 4 22.151 42.705 6.945 1.00 3.69 C
ATOM 91 CG1 ILE C 4 21.583 41.559 6.110 1.00 4.63 C
ATOM 92 CG2 ILE C 4 23.672 42.799 6.774 1.00 0.94 C
ATOM 93 CD1 ILE C 4 21.832 41.708 4.619 1.00 5.50 C
TER
ATOM 2076 N GLN D 1 -5.202 -31.148 19.518 1.00 7.90 N
ATOM 2077 CA GLN D 1 -4.657 -29.990 20.288 1.00 8.01 C
ATOM 2078 C GLN D 1 -3.890 -30.442 21.508 1.00 6.88 C
ATOM 2079 O GLN D 1 -3.784 -29.715 22.500 1.00 7.19 O
ATOM 2080 CB GLN D 1 -5.777 -29.086 20.761 1.00 9.28 C
ATOM 2081 CG GLN D 1 -5.605 -27.661 20.342 1.00 1.13 C
ATOM 2082 CD GLN D 1 -6.792 -27.230 19.563 1.00 2.49 C
ATOM 2083 OE1 GLN D 1 -7.914 -27.444 20.008 1.00 3.58 O
ATOM 2084 NE2 GLN D 1 -6.574 -26.639 18.389 1.00 3.22 N
ATOM 2085 N LYS D 2 -3.368 -31.653 21.440 1.00 5.19 N
ATOM 2086 CA LYS D 2 -2.612 -32.197 22.545 1.00 3.61 C
ATOM 2087 C LYS D 2 -1.686 -33.248 21.993 1.00 1.53 C
ATOM 2088 O LYS D 2 -2.009 -33.946 21.031 1.00 1.89 O
ATOM 2089 CB LYS D 2 -3.545 -32.831 23.588 1.00 4.00 C
ATOM 2090 CG LYS D 2 -4.381 -31.846 24.404 1.00 4.19 C
ATOM 2091 CD LYS D 2 -5.747 -32.442 24.727 1.00 5.42 C
ATOM 2092 CE LYS D 2 -6.619 -31.499 25.543 1.00 5.82 C
ATOM 2093 NZ LYS D 2 -6.281 -31.538 26.993 1.00 5.55 N
ATOM 2094 N THR D 3 -0.512 -33.331 22.592 1.00 9.45 N
ATOM 2095 CA THR D 3 0.451 -34.328 22.187 1.00 7.41 C
ATOM 2096 C THR D 3 -0.247 -35.666 22.381 1.00 6.63 C
ATOM 2097 O THR D 3 -1.086 -35.814 23.270 1.00 6.24 O
ATOM 2098 CB THR D 3 1.689 -34.276 23.070 1.00 6.49 C
ATOM 2099 OG1 THR D 3 2.475 -33.141 22.697 1.00 5.74 O
ATOM 2100 CG2 THR D 3 2.505 -35.558 22.932 1.00 5.93 C
TER
END
Example 3. Residue-Residue contact prediction
(A) An example of the RR format for monomeric targets
PFRMAT RR
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC # <- entire target sequence (up to 50
HDFGRTYIWQMSDASHMD # residues per line)
1 8 0 8 0.720
1 10 0 8 0.715 # <- i=1 j=10: indices of residues (integers),
31 38 0 8 0.710
10 20 0 8 0.690 # <- d1=0 d2=8: the range of Cb-Cb distance
30 37 0 8 0.678 # predicted for the residue pair (i,j)
11 29 0 8 0.673
1 9 0 8 0.63 # <- p=0.63: probability of the residues i=1 and j=9
21 37 0 8 0.502 # being in contact (in descending order)
8 15 0 8 0.401
3 14 0 8 0.400
5 15 0 8 0.307
7 14 0 8 0.30
END
(B) An example of the RR format for multimeric targets
PFRMAT RR
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL 1
HLEGSIGILLKKHEIVFDGC
HDFGRTYIWQMSD
A1 B9 0 8 0.70
A1 B10 0 8 0.70 # <- i=1 j=10: indices of residues: Ai and Bj,
A1 B12 0 8 0.60
A1 B14 0 8 0.20
A1 B15 0 8 0.10
A1 B17 0 8 0.30
A1 B19 0 8 0.50
A2 B8 0 8 0.90
A3 B7 0 8 0.70
A3 B12 0 8 0.40
A3 B14 0 8 0.70
A3 B15 0 8 0.30
A4 B6 0 8 0.90
A7 B14 0 8 0.30
A9 B14 0 8 0.50
END
Example 4. Estimates of model accuracy prediction
(A) Global Model Quality Score
PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
METHOD Description of methods used
MODEL 1
QMODE 1
3D-JIGSAW_TS1 0.8
FORTE1_AL1.pdb 0.7
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 Error estimate is CA-CA distance in Angstroms
METHOD Description of methods used
MODEL 1
QMODE 2
3D-JIGSAW_TS1 0.8 10.0 6.5 5.0 2.0 1.0
5.0 4.3 4.6
FORTE1_AL1.pdb 0.7 8.0 5.5 4.5 X X
4.5 4.2 5.0
END
|
