13th Community Wide Experiment on the
Critical Assessment of Techniques for Protein Structure Prediction

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Submission Rules and Format

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 'O'). 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)

  • CASP13 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 server-specific parameters will be taken from your server registration form.
    For the servers participating in assembly prediction, we will be sending additionally the STOICHIOMETRY variable specifying type of the quaternary structure expected, e.g. A1 for a monomer, A3 for a homotrimer, A3B1 for a tetramer consisting of a homotrimer and a monomer. The SEQUENCE variable for heteromeric targets will be provided in the FASTA format like
    >H9999 description containing subunit 1 and ending with |
    FASTASEQVENCEFORFIRSTSVDVNIT
    >H9999 description containing subunit 2 and ending with | 
    FASTASEQVENCEFORSECENDSVDVNIT
    
  • 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 CASP13 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 
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 hetero-ultimeric 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


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