David Baker, University of Washington
Nick Grishin, University of Texas
David Jones, University College, London
Justin MacCallum, University of Calgary
Michael Sternberg, Imperial College, London
- Predictions in CASP12 may be submitted in 4 formats:
TS # Atomic coordinates
RR # Pairs of residues in contact
QA # Model accuracy assessment
IA # Interface accuracy assessment
Note. IA category has been announced on June 20, 2016.
- One team may make a prediction of a target by submitting up to five models
in the TS categories, one model in the RR and IA categories 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 as well as refinement and data-assisted
targets should be submitted in the TS format. Input data for contact-assisted
predictions will be provided in the RR format; a starting model for the refinement
will be selected from among the best server models.
- 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 CASP12
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 CASP12 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 CASP12 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.
-
Multimeric predictions may be sent for all targets.
-
Interface accuracy predictions may be sent for all multimeric targets, including homomultimers and heteromultimers.
In CASP12, IA predictions should be sent on all applicable targets between July 1 and July 22.
Submission rules for server groups (3-day deadline in TS and RR categories, 2 day deadline for QA)
-
CASP12 queries will be sent to the registered servers from the CASP distribution
server casp-meta AT predictioncenter.org. Email servers are advised
to reply to this address immediately upon receiving the query with an acceptance
email with subject: "T0xxx - 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).
For the servers participating in model accuracy assessment and data-assisted
categories, we will be sending the TARBALL-LOCATION
variable instead of (or in addition to, if you specify so) the SEQUENCE.
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.
-
TS and RR 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 CASP12 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 (or 2 and higher for RR
category). In QA category either model 1 or model 2 will be accepted
depending on the stage of the QA request (see the General Rules above or description
of the MODEL record below).
-
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. The facility that
allows checking accepting predictions from servers is available from our website.
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, IA
TARGET Target identifier from the CASP12 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
PFRMAT QA
QA indicates that submission contains estimates of model accuracy
PFRMAT IA
IA indicates that submission contains prediction of interchain interfaces
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 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 INTERFACE is required only for the submissions in the IA format.
INTERFACE record provides names of chains forming the interface.
The INTERFACE record should be placed as the first record of an
INTERFACE - TER block in the IA prediction.
INTERFACE AB
Indicates that data below correspond to the interface between chains A and B.
Record TER is used to terminate an independent segment of structure
in TS prediction categories or data block for a specific interface in IA category.
In TS predictions, every TER record should correspond to the preceding PARENT
record in the model.
Using of only one PARENT-TER block within a TS prediction
is strongly encouraged in CASP12.
In IA prediction, every TER record should correspond to the
preceding INTERFACE record in the model.
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 CASP12 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). Using of only one
PARENT-TER block within a prediction is strongly encouraged.
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. We require predictors to submit their error estimates for own
predictions as these results will be separately evaluated in the quality
assessment category. 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 2).
The sequence should be followed by the list of contacts in the
five-column format:
i j d1 d2 p
Notes (see Example 2):
- 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).
Interface accuracy prediction (PFRMAT IA).
In this category predictors are asked to provide the probability of specific
residues belonging to the interchain interface(s). Residues will be
considered to be in the interface if the distance between the closest
heavy atoms in the residues belonging to different chains is below
5 Angstroems.
Data in this format are inserted between MODEL and END records of the
submission file and should be provided separately for each predicted
interface (usually - pair of chains) as an INTERFACE - TER block.
Data in each interface block should start with the keyword INTERFACE
and terminated with a TER card (see Example 5).
You may submit your estimates of residues belonging to different interfaces
in one of the two different modes - IMODE 1 or IMODE 3. Keyword IMODE
should be placed in the IA predictions immediately before the first MODEL keyword.
IMODE 1 : probability of residues being in interface
of own quaternary structure models.
IMODE 3 : probability of residues being in interface
predicted from sequence alone.
The prediction should contain a list of predicted interface residues in
in the two-column format:
res p
Notes:
- the string res identifies a residue in the interface and should be provided
in the form A123, where A is chain ID and 123 is a residue number within
the range of the target sequence length.
- the real number p indicates probability of the residue belonging to the
interface between two chains and should be in the range 0.0 - 1.0.
Probability values larger than 0.5 identify residues that are predicted
to be more likely in the interface than not. In binary (two-class)
evaluations, the value of 0.5 may be considered as the cutoff separating
residues predicted to be in the interface from those that are not.
- any residue NOT included in the prediction is assumed to have the probability
of 0 of belonging to the interface.
- data for each predicted interface in the multimolecular complex should be
separated by the TER cards (see Example 5).
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 casp12 archive page (http://predictioncenter.org/download_area/CASP12/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 casp12 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 casp12 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 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 CASP12 format used for tertiary structure prediction
(A) An example of 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
(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 T0999
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
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
Example 3. Multichain predictions
(A) An example of 3D atomic coordinates model 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 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 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
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
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
Example 5. Interface accuracy prediction
(A) Single interface
PFRMAT IA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
IMODE 1
MODEL 1
INTERFACE AB
A1 0.70
A2 0.60
A3 0.45
B12 0.80
B13 0.70
B14 0.30
TER
END
(B) Multiple interfaces between pairs of chains
PFRMAT IA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
IMODE 1
MODEL 1
INTERFACE AB
A1 0.70
A2 0.60
A3 0.45
B12 0.80
B13 0.70
B14 0.30
TER
INTERFACE AC
A1 0.70
A2 0.60
A3 0.45
C121 0.60
C122 0.55
C141 0.30
TER
INTERFACE BC
B11 0.70
B12 0.60
B13 0.45
C30 0.80
C31 0.70
B44 0.30
TER
END
(C) Complex interface involving more than 2 chains
PFRMAT IA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
IMODE 3
MODEL 1
INTERFACE ABC
A1 0.70
A2 0.60
A3 0.45
B12 0.80
B13 0.70
B14 0.30
C121 0.60
C122 0.55
C141 0.30
TER
END