General submission rules
- Models from both regular groups and servers should be submitted directly by e-mail to
casprol AT predictioncenter.org or using
the CASP ROLL model submission facility
.
- Predictions for CASP ROLL may be submitted in 2 separate formats:
TS # 3D atomic coordinates (Tertiary Structure) prediction
RR # Residue-Residue separation distance prediction
- One team may make a prediction of a target by submitting
up to five models in TS or RR formats.
- 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 submission file should contain prediction for only one target.
- Each submission file should contain only one of the allowed format categories.
- Each submission file may contain either one or several models in the same
prediction category. 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 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 target has expired.
- Each submitted model is automatically verified by the format verification
server. In case of successful submission no confirmation email will be sent.
A unique ACCESSION CODE is composed from the number of the target, prediction
format category, prediction group number, and model index.
Example:
Accession code R0001TS005_2 has the following components:
R0001 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 ROLL
web page.
If the submission contains an error, 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 specific to regular group predictions (3+ week deadline)
-
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 ROLL 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.
-
When sending predictions by email, please remember to use as an origination point
only the email address registered with the Prediction Center (make sure we have
the updated email address for you on file - check for this your "My Personal Data"
link from our menu). If you cannot use the registered email address for submission,
please use the
submission form instead
.
-
Time for returning regular predictions is set separately for each target
through the Target List form. Usually regular predictors have around 3 weeks
from the date of target release to return a prediction. For the most difficult
targets this period may be prolonged.
Submission rules specific to server group predictions
-
CASP ROLL queries will be sent to the registered servers from the CASP distribution
server casprol-meta AT predictioncenter.org. Email servers are requested
to reply to this address immediately upon receiving the query with an acceptance
email with subject: "R0xxx - query received by MY_SERVER". This will help us to
track whether your server received a request from us so that we can timely address
any connectivity issues. Please do not send your predictions to this address as
they will be ignored.
-
We will be sending 3 variables to your server's submission URL (or email):
the SEQUENCE, the TARGET-NAME and the REPLY-E-MAIL (where to return the results).
Names for these server-specific parameters will be taken from your server
registration form.
- Server models should be returned automatically to the address specified in the
REPLY-E-MAIL field of the query.
Please note that the return address should be always taken from our query and not
hard-coded as we may change it during the season.
-
Servers are requested to return predictions in 72 hours from the target release time.
No additional time for corrections will be allotted, but corrections will be accepted
within the original 72 hour 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 ROLL 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.
Predictions in attachments to the emails will be rejected. 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.
-
The submission engine will resend the query if it encounters obvious connecting problems
(network timeouts, 'no response' etc.). Failures that go beyond that require special attention,
but we'll make every effort to notify server curators ASAP if we suspect something is
not working.
Format description
All submissions 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
TARGET Target identifier from the CASP ROLL 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 independent segments of structure in the 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
Record TARGET should appear on the second line of the prediction and
is used for all submissions.
TARGET Rxxxx
Rxxxx 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 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 methods used. Predictors are urged to provide
as full a description of the methods as possible, including references,
data libraries used, and values of default and non-default parameters.
These descriptions will be made available via the Prediction Center WEB
pages as well as printed along with the other materials distributed at the
meeting. Length of 100 - 500 words is suggested.
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 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.
Record PARENT is required only for the submissions in the TS format.
PARENT record indicates structure templates used to generate any independent
segment of MODEL (see description of the TS format below).
The PARENT record should be placed as the first record of any such independent
segment. Only one PARENT record per structure segment is allowed. For multimeric
predictions only one PARENT record per whole structure is allowed.
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 or the independent segment of structure 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. Subdomains of the target structure found
to correspond to different known folds may be submitted as independent
segments of structure with reference to only one PDB chain per segment.
Record TER is used to terminate an independent segment of structure
(PFRMAT TS). Every TER record should correspond
to the preceding PARENT record in the model.
TER
3D 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 ROLL target table).
Coordinates for each model or an independent structure segment should begin
with a single PARENT record and terminate with a TER record (see above).
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.
Specifically, if only CA atoms are predicted by the method, predictors are
encouraged to build the main chain atoms for every residue before submission
to CASP. One program that can make such a conversion is
Maxsprout server
of Liisa Holm and co-workers. (If only CA atoms were submitted it would not be
possible to run most of the analysis software, which would severely limit the
evaluation of that prediction.)
When multiple independent segments of structure are used in a prediction,
they will be evaluated separately with no assumption of a common
frame of reference between the segments. For any given MODEL, no target
residue may be repeated among all such independent structure segments.
Even though all of the independent PARENT-TER frames will be evaluated,
only the best scoring frame will contribute to the group score on any
given evaluation domain. Potential multi-domain nature of targets will be
addressed in the evaluation even if the prediction
is made in a single frame of reference (i.e. without separation into multiple
segments of structure).
For quaternary structure predictions, coordinates for all chains should be submitted
in the same frame of reference and therefore only one PARENT - TER section is allowed
per prediction. This means that no TER record should separate different chains
(this is different from the PDB!). First chain should be labeled as A and all
the subsequent chains should follow the latin alphabet, e.g., tetramer's chains should
be labeled as A, B, C, D.
There will be no announcements or assignments of targets to
oligomeric prediction category. Instead, for every target
you can submit either tertiary structure prediction or quaternary
structure prediction. There is no need to submit monomer in addition to a multimer:
we will automatically extract coordinates of the first chain from the quaternary
prediction and save it as a monomer for future mainstream evaluation alongside
with monomers submitted by other groups. Multimeric predictions will be evaluated
separately. Tentative oligomeric state of the protein (if provided by the
experimentalists) will be announced through our Target List page, but it is up to
predictor to decide what oligomerization state the protein is in.
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. If your method can not produce these estimates - please put some
high number (e.g., "99.9") in that field. We strongly encourage predictors
to submit their error estimates for own predictions as these results will be
separately evaluated in the quality assessment category.
Residue-Residue separation prediction (PFRMAT RR).
Data in this format are inserted between MODEL and END records of the
submission file.
Format for the predicted separation distance between pairs of residues.
The distance is defined as the separation between C-beta atoms (C-alpha for
glycine residues).
The (five column) RR format:
i j d1 d2 p
Notes (see Example 2):
- entire target sequence should be split over multiple lines with a
maximum of 50 residues per line
- for intrachain residue-residue contacts residue number indices
i and j should be used for distance specification (i < j), i.e.
only one diagonal of the separation matrix should be supplied
- the distances d1 and d2 (real numbers) should indicate the range of
Cb-Cb distance predicted for the residue pair (C-alpha for glycines)
- the real number p should range from 0.0 - 1.0 to indicate
probability of the distance falling between the predicted range
- residue 'contacts' (defined here - as in CASP2 - as Cb-Cb<8A) can be
predicted with this format as:
i j 0 8 p
- any pair NOT listed is assumed to be NOT considered by predictor
- for multichain predictions residue indices should be composed of
chain ID and residue number, e.g. A2, B44 (see Example 4B).
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 ROLL format used for tertiary structure prediction
(A) An example of TS prediction.
PFRMAT TS
TARGET R9999
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
(B) A model consisting of 2 independent structure segments (could be a target
modeled from two PDB domains, where relative orientation is unknown;
could be 2 fragments predicted by ab initio methods - ab initio example shown).
In a single MODEL no residue should appear twice among all such segments.
PFRMAT TS
TARGET R9999
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 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 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
PARENT N/A
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
TER
END
Example 2. Residue-Residue contact prediction
The flexibility offered by the new format allows algorithms
parameterized to predict any distance range to be used.
Below is an example of how to use the new residue-residue separation
distance format to submit a prediction of residue contacts defined as Cb-Cb
distances < 8 A.
PFRMAT RR
TARGET R9999
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
HDFGRTYIWQMSD # residues per line)
1 9 0 8 0.70
1 10 0 8 0.70 # <- indices of residues: i and j (integers),
1 12 0 8 0.60 # <- the range of Cb-Cb distance predicted
1 14 0 8 0.20 # for the residue pair: d1 and d2 (real),
1 15 0 8 0.10 # <- probability of the distance between
1 17 0 8 0.30 # Cb atoms being within the specified
1 19 0 8 0.50 # range: p (real)
2 8 0 8 0.90
3 7 0 8 0.70
3 12 0 8 0.40
3 14 0 8 0.70
3 15 0 8 0.30
4 6 0 8 0.90
7 14 0 8 0.30
9 14 0 8 0.50
END
Example 4. Multichain predictions
(A) An example of 3D atomic coordinates model prediction.
PFRMAT TS
TARGET R9999
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
REMARK
REMARK Predictors should NOT use TER separator between chains
REMARK
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
(B) An example of how to use the RR format to submit a prediction of
interchain (chains A and B) residue-residue contacts defined as Cb-Cb
distances < 8 A.
PFRMAT RR
TARGET R9999
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
HDFGRTYIWQMSD # residues per line)
A1 B9 0 8 0.70
A1 B10 0 8 0.70 # <- indices of residues: Ai and Bj,
A1 B12 0 8 0.60 # <- the range of Cb-Cb distance predicted
A1 B14 0 8 0.20 # for the residue pair: d1 and d2 (real),
A1 B15 0 8 0.10 # <- probability of the distance between
A1 B17 0 8 0.30 # Cb atoms being within the specified
A1 B19 0 8 0.50 # range: p (real)
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
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