16th 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 CASP16 may be submitted in 3 formats:
      TS    # Atomic coordinates (tertiary or quaternary structure) 
      QA    # Model accuracy assessment
      LG    # Ligand prediction 
    

  • One team may make a prediction of a target by submitting up to five models in the TS or LG categories, and one model in the QA category.
  • Submissions for monomeric targets, assembly targets, protein-ligand complexes, nucleic acid structure, and data-assisted targets should be submitted in the TS format.
  • Each submission file should contain predictions for only one target.
  • Each submission file should contain only one of the allowed format categories.
  • Submission files in QA category 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.
    Note. Real time format verification does not apply to LG predictions (see below), which will be verified only after all models on ligand targets are collected.
  • In case of successful submission no confirmation email is sent. A unique model ACCESSION CODE is assigned to each accepted model. The 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:
         T0444   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 CASP16 web page.
    If the submission contains an error, the regular group leader or server contact person will be immediately notified through email. If your prediction is rejected for format inconsistency, you will have the possibility to correct problems and re-send prediction(s) within the target prediction time window.

Submission rules for expert groups (usually, 3-week deadline in TS category, 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 CASP16 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 CASP16 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.
  • Deadline for returning regular group predictions is set separately for each target. Usually regular deadline predictors have around 3 weeks from the date of target release to return a prediction.
  • Predictions in TS categories should be normally sent only on all-group targets.
  • Predictions in LG format should be sent for targets where Additional Information and Ligand fields in the target-specific Target List pages indicate availability of ligands.
  • Predictions in TS categories should contain residue confidence estimates in the column reserved for the B-factor value in the PDB format.
  • Predictions in QA category should be sent for all multimeric targets.
  • Multichain predictions should be sent for heteromeric targets (names starting with 'H') and homo-oligomeric targets (names starting with 'T' and stoichiometry parameter other than A1). The stoichiometry information for each target will be provided in the column 'Stoichiom' in the Target List page.

Submission rules for server groups (3-day deadline in TS categories, 2 day deadline for QA)

  • CASP16 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 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 CASP16 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 QA category).
  • 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 must start with a CASP header. Records in the header must begin with a standard keyword starting in the first column of the line. The mandatory records should be listed in the following order:
PFRMAT     Format specification code:  TS , QA, LG
TARGET     Target identifier from the CASP16 target table
AUTHOR     XXXX-XXXX-XXXX   Registration code of the Group Leader or Server Group Name 
METHOD     Records describing the methods used
MODEL      Beginning of the data section for the submitted model
...
END        End of the submitted model
Some header records are specific to prediction categories and should follow the first five mandatory records specificed above.
PARENT     TS category, mandatory. Specifies templates used to generate the model.
TER        TS category, mandatory. Terminates chain in a TS model.
SCORE      TS category, optional. Reliability of the model (overall fold).
QSCORE     TS category, optional. Reliability of the interfaces in the quaternary structure of the model.
STOICH     TS category, optional. Predicted stoichiometry of an assembly target (in the form AiBjCn).
LIGAND     LG category, mandatory for pose prediction. Ligand id and name starting ligand coordinate section.
LSCORE     LG category, optional. Reliability of the ligand and binding pocket pose.
AFFNTY     LG category, optional for pose prediction. Predicted affinity or ranking.
REMARK     All categories, optional. Comment record. May appear anywhere after the first 3 required lines, but not within the MDL block of an LG prediction.
QMODE      QA category, mandatory. Specifies type of the QA prediction.
Models should be submitted in Plain Text format.


PFRMAT record should appear on the first line of the prediction and is used for all submissions.

PFRMAT TS
     TS  indicates submission containing 3D atomic coordinates
         in standard PDB format

PFRMAT QA
     QA  indicates submission containing estimates of model accuracy

PFRMAT LG
     LG  indicates submission containing 
       3D atomic coordinates of the protein receptor in standard PDB format, 
       3D atomic coordinates of ligand in standard MDL format 
       (https://en.wikipedia.org/wiki/Chemical_table_file),
          and /or  
       the predicted affinity (absolute/relative/rank) for the protein-ligand complex. 


TARGET record should appear on the second line of the prediction and is used for all submissions.

TARGET Txxxx
     Txxxx indicates id of the target predicted.


AUTHOR record 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

METHOD records are used for all submissions.
These records describe the method used. Predictors are urged to provide a concise description of the method, github links, including data libraries used, and values of default and non-default parameters.


MODEL record is used for all submissions.
Signifies the beginning of model data.
For pharmaceutical ligand predictions, one MODEL is one predicted pose and/or one predicted affinity for a given receptor-ligand pair.

MODEL  n  
       n        Model index n is used to indicate predictor's ranking
                according to her/his belief which TS/LG model is closest to the 
                target structure (1 <= n <= 5). In CASP16, predictors can 
                additionally submit model 6 based on the MSA provided by the organizers.   
                Model index is included automatically in the ACCESSION CODE. 
                All models with index higher than 6 will be discarded. 
Model index should be set to 1 in QA category.


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.


SCORE Used in TS predictions. This record specifies a model reliability score in range [0.0, 1.0] which will be evaluated in the EMA self-assessment. Reflects similarity of the full model/complex to the target upon global superposition (GDT/TM style). Independently from that value, the average per-residue scores derived from the B-factors will be evaluated against full-atomic superposition-independent scores.


QSCORE Used in assembly predictions. Optional. This record specifies a quaternary structure reliability score (interface accuracy) in range [0, 1] which is evaluated in EMA self-assessment. Will be evaluated against interface contact-based scores (e.g. DockQ, QS-score).


STOICH Used in assembly predictions. Optional. This record specifies predicted stoichiometry of the target in the form AiBjCn... Should be placed after the MODEL keyword and correspond to the stoichiometry of model coordinates.

STOICH A2B2C4D4


PARENT record is required for 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. 


TER record is required in TS predictions to indicate chain termination.

TER


QMODE record is required in QA predictions to indicate type of prediction.

QMODE n
     n=1 :      global model quality scores (MQS - two numbers per model)
     n=2 :      MQS and interface reliability estimates on per-residue basis.


LIGAND record is required for ligand pose prediction in LG format. It indicates the beginning of the ligand coordinate data block. Coordinates for each ligand should be submitted under a separate LIGAND record.

LIGAND n XXX
      n         Ligand number as provided in the SMILES file accessible 
                  from the target-specific Target List page.
      XXX       Ligand name as provided in the released SMILES file.
   


LSCORE Used in LG predictions. Optional. This record specifies a ligand and binding pocket reliability score (prediction accuracy) in range [0, 1] which is evaluated in EMA self-assessment. Will be evaluated against interaction-based scores (e.g. lDDT-PLI). Must appear immediately after the LIGAND record and before the MDL coordinate block.


AFFNTY Used in LG predictions. Optional. This record specifies score(s) that correlates with the binding affinity of the protein-ligand complex. Will be evaluated against binding affinity correlates (e.g Kd, IC50). Must appear after the last LIGAND coordinate block.

AFFNTY x type
	type=aa : ABSOLUTE AFFINITY (real): Predicted binding affinity for the receptor protein, 
             expressed as a dissociation constant (Kd) in nanomoles/liter (nM).
	type=ra : RELATIVE AFFINITY (real): Predicted binding affinity of this ligand 
	     for the receptor protein relative to a user-selected reference 
             ligand in the series for this protein, expressed as a ratio of 
	     dissociation constants: Kd/Kd(ref).
	type=lr : LIGAND RANK (integer): predicted rank of this ligand for the receptor protein 
             among those in the series for this protein with 1 implying 
             highest affinity, i.e., lowest dissociation constant.
The affinity estimates should be provided in one of the three forms, in the following priority.

1. If your method can estimate absolute affinity (aa), please provide that, e.g.

AFFNTY 0.050 aa
2. If you cannot provide aa, then provide relative affinity (ra), e.g.
AFFNTY 0.900 ra
3. If you cannot provide aa or ra, please provide ligand rank (lr), e.g.
AFFNTY 1 lr


END record is used for all predictions and indicates the end of a single model submission.


Atomic coordinates (proteins) (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 CASP16 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 atoms, i.e. the N, CA, C and O atoms of every residue.

For any given MODEL, no target residue may be repeated in the prediction.

For assembly prediction (Example 2), coordinates for all chains should be submitted in one PDB-like file. Chains should be labeled 'A', 'B', ... according to the provided template for each target. The convention for chain order is: alphabetical, heteromeric units (different sequences) first. For example, for a homotrimer of heterodimers please name chains in the following order: AB (first hetero-dimer), CD (second dimer), EF (3rd dimer). Names of heteromeric targets will start with letter 'H', e.g. H0960, names of all other regular targets will start from letter 'T', e.g. T1001. Homo-multimeric predictions are encouraged for all other regular targets, if applicable. If subunits of heteromeric targets are additionally released as separate tertiary structure prediction targets, there will be no need to submit monomeric predictions in addition to multimeric: we will automatically extract coordinates of each first different chain from the assembly prediction and save it as a tertiary structure model for the corresponding subunit. Information on the tentative oligomeric state of the protein (the stoichiometry formula to the best of our knowledge at the time of target release), will be announced through the Target List page. If a prediction is for protein-RNA complex, protein chains should be named alphabetically and RNA chains numerically.

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, percentage-scale confidence estimates (0-100) should be provided (100.00 for highly confident prediction). The estimates should assess accuracy of the relative positions of atoms in the neighborhood (incl. other chains in the case of complexes). Evaluation will be based on full-atomic superposition-independent scores (e.g. lDDT, CAD) on the level of residues, i.e. a residue confidence estimate is derived from averaging the confidence values of all its atoms. Models with all residues having the same 'B-factor' will be rejected.


Atomic coordinates (RNA) (PFRMAT TS, target name starting from 'R' for RNA structures and 'M' for protein-RNA complexes).
A CASP RNA submission may contain up to five RNA 3D models in the RNA-Puzzles community standard pretexted by the CASP keywords (see Format Description section above, and Example 3).
Coordinates should be provided for all nucleotides provided in the target FASTA file. Only standard nucleotides (A, C, U, and G) should be used. Modified nucleotides will be treated as unmodified ones. All additional atoms will be discarded. Only the following atoms will be considered:
(1) for nucleobases: C2, C4, C6, C8, N1, N2, N3, N4, N6, N7, N9, O2, O4, and O6 (2) for sugar-phosphate backbones: C1', C2', C3', C4', C5', O2', O3', O4', O5', OP1, OP2, and P [1].

CASP will provide RNA sequence (in the FASTA format) of the target through the target-specific web page from the Target List page.
FASTA header will contain target ID (e.g., T1001) and chain ID (number from 0 to 9) for every different strand in the structure. Body of the FASTA file will contain nucleic acid sequence, e.g.
> T1001 0
GGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUUC

CASP will provide a 3D structure template for the target through the target-specific web page from the Target List page.
We will generate a PDB template for each RNA target using the rna_puzzles_format.py script from package [2]:
python rna_puzzles_format.py [FASTA file] > [Template.pdb]
All predictions should comply with the provided PDB template. To ensure correctness of your RNA 3D prediction [2], you can run
python format_check.py [Prediction.pdb] [Template.pdb] .
The script verifies: (1) the expected number of residues and atoms included in the particular prediction (all hydrogens must be discarded) and (2) ordering of residues and atoms with respect to the template. If a prediction is in correct format (i.e., it contains all required nucleotides and their atoms in the requested order), the script will finish with a success message, otherwise an error message will be generated and written to 'xx.format_check.txt' file.

If you have a complete 3D prediction and want to bring it to the RNA-Puzzles community standard, you can use the rna-tools package [3] provided within the RNA-Puzzles toolkit [4]. Please run:
rna_pdb_toolsx.py --get-rnapuzzle-ready *pdb --inplace

For protein-RNA complexes, protein chains should be named alphabetically (A,B,C,...) while RNA strands numerically (0,1,2,...) - see Example 4.

References:
[1] Cruz, J. A., Blanchet, M. F., Boniecki, M., Bujnicki, J. M., Chen, S. J., Cao, S., ... & Westhof, E. (2012). RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Rna, 18(4), 610-625.
[2] https://github.com/chichaumiau/RNA-Puzzzles_format
[3] https://github.com/mmagnus/rna-tools
[4] Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao, Y., ... & Miao, Z. (2020). RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic acids research, 48(2), 576-588.


Ligand/receptor atomic coordinates and/or affinity (PFRMAT LG).

Targets in Ligand prediction category can be of two types: (1) regular tertiary structure or assembly targets containing incidental ligands (target names starting with T, H or M, e.g. T1999), and (2) targets of pharmaceutical interest intended exclusively for ligand pose and/or affinity prediction (names starting with L, e.g. L1000).

Information on the known ligands and suggested prediction tasks will be communicated to predictors through the Additional Information field in the target-specific Target List pages, and also provided as a text file (so-called SMILES file) in the form

ID  Name SMILES                        Task
001 LIG  CC(C)N1CCN(CC1)C(=O)C2=CC=CS2 PA
002 LIG  CC(C)N1CCN(CC1)C(=O)C2=CC=CS2 PA 
Note: For L-targets we will provide tar-gzipped SMILES file for 'supertargets' encompasing a set of targets, each representing a different ligand (or a ligand set) for the same receptor protein. For example, a supertarget L1000 will include targets L1001 (receptor 1, ligand set 001), L1002 (receptor 1, ligand set 002), and so on.

The ligand ID and name provided in the first two columns of the information file should be used in the LIGAND field of an LG prediction. The SMILES column provides the canonical SMILES string for each ligand. The Task column suggests prediction tasks for modelers (P:pose, A:affinity, PA: pose and affinity).

A prediction in the LG format can contain 3 blocks in order: (1) coordinates of the protein receptor (in CASP TS format description above), (2) coordinates of the ligand in the same frame of reference as the receptor (in MDL format described below), and (3) the affinity record.
For pose prediction (P-tasks), a prediction must contain coordinates of the receptor and the ligand (blocks 1+2, Example 6.1). For affinity predictions (A-tasks), a prediction must contain the affinity record (block 3, Example 6.2). For prediction of both pose and affinity (PA-tasks), a prediction should be in one of the three forms: blocks 1+2+3 (Example 6.3), blocks 1+2, or block 3.

Each LIGAND record in an LG prediction starts a data block specific to the ligand ID.

 LIGAND 001 LIG
The ligand number in this record indicates that the subsequent data block is for the ligand '001' from the SMILES file. Note that in the provided above example there are two instances of the same ligand LIG (001 and 002), and each of the instances should be submitted under a separate LIGAND record in the LG prediction.

Blocks of information for each LIGAND should contain data in the MDL format. Predictors should ensure that atoms are properly connected by bonds in the Bonds block, according to the definition of the ligand given by the canonical SMILES string. Submissions with incorrect connectivity will be marked as invalid. Hydrogen atoms are optional and can be omitted.

MDL Format description

Ligand coordinates should be submitted in MDL format and must include the following information:
    - Header block
    - Counts line
    - Atom block
    - Bonds block
    - End line
    - Model delineation line 
Templates for submitting ligands can be generated with the template_gen.py script (Usage: python template_gen.py ) N.b the script uses RDKit to canonicalise SMILES strings and generate output. Instructions for installing RDKit can be found here:
    https://www.rdkit.org/docs/Install.html
Header block
    Consists of three lines. 
    The first is the title line, which can be blank but must exist. 
    The second line is the Program/ time stamp line 
	(The name of the program used for structure generation). 
    The third is a blank line.
Counts line
    The counts line is a series of 11 entries e.g.

     17 18  0  0  0  0  0  0  0  0999 V2000

    The first two numbers are required and denote the number of 
    atoms and bonds in the file respectively. 
Atom block
    There should be a single entry on each line for every atom in the structure.
    The first three entries are 10 characters each and specify 
    the atom coordinates in the x, y , and z dimensions, respectively.

    Atom coordinates are followed by a space and the chemical symbol of the atom. 
    The chemical symbol is followed by a number of entries relating to chemical 
    properties. These may be left as zeros.
Bonds block
    There should be a single entry on each line for every bond in the structure. 
    The important numbers are the first number that represents the first atom number 
    in the bond, the second number representing the second atom in the bond, 
    and the third number representing the bond type. 

    Bond types are denoted as follows: 

    1= Single, 2 = Double, 3 = Triple, 4 = Aromatic,
    5 = Single or Double, 6 = Single or Aromatic, 7 = Double or Aromatic, 8 = Any. 
End line
    The bonds block must be immediately followed by a line denoting 
    the end of the model as such:

    M  END


Estimation of model accuracy (PFRMAT QA).

In QA category, predictors are requested to use model index '1' for predictions.

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 scores (MQS - two numbers per model)
QMODE 2 :   MQS and interface reliability estimates on per-residue basis.

The first line of data should specify mode identifier, i.e. QMODE (see Example 5).

QMODE1 (Example 5A): The first column in each line contains model identifier (file name of the accepted 3D prediction). The second and third columns contain two accuracy scores for a model. The accuracy scores are real numbers in range [0.0, 1.0] (1.0 being a perfect model) predicting overall fold accuracy (i.e. a score conceptually similar to the self-estimated SCORE value in the TS format, see above) and overall interface accuracy (a score conceptually similar to the self-estimated QSCORE value in the TS format). If you do not provide the interface accuracy estimate (second MQS number), please put 'X' in place of the score.

QMODE2 (Example 5B): If you additionally provide estimates of residues being in the interface, you should provide confidence scores in range [0.0,1.0] for all interface residues observed in the model. These should be provided additionally to the information provided in QMODE1 (see Example 5B). Interface residues are defined as having a contact with at least one residue from another chain (CB-CB distance <=8A, CA in case of Glycine). The confidence relates to the probability of an atom being in the actual interface of the native structure in the format [chain_name][res_num]:[confidence_score] (e.g. A26:0.90).

Note. Please, be advised that a QA record line n QMODE2 may be too long to fit all interface residues, 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.


Example 1. Atomic coordinates (Tertiary Structure)

The primary CASP16 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 90.00
ATOM      2  CA  GLU     1       9.623  -9.833   1.984  1.00 85.50
ATOM      3  C   GLU     1       8.913 -11.104   1.521  1.00 85.50
ATOM      4  O   GLU     1       9.187 -11.630   0.461  1.00 80.00
ATOM      5  CB  GLU     1       8.814  -8.614   1.546  1.00 85.45
ATOM      6  CG  GLU     1       7.372  -8.754   2.039  1.00 75.00
ATOM      7  CD  GLU     1       7.339  -8.625   3.562  1.00 93.50
ATOM      8  OE1 GLU     1       8.370  -8.307   4.131  1.00 90.50
ATOM      9  OE2 GLU     1       6.284  -8.846   4.132  1.00 85.40
ATOM     10  N   THR     2       7.998 -11.599   2.304  1.00 70.60
ATOM     11  CA  THR     2       7.266 -12.832   1.907  1.00 75.60
ATOM     12  C   THR     2       6.096 -12.456   1.005  1.00 76.40
ATOM     13  O   THR     2       5.008 -12.217   1.466  1.00 75.60
ATOM     14  CB  THR     2       6.731 -13.533   3.157  1.00 70.90
ATOM     15  OG1 THR     2       7.662 -13.379   4.220  1.00 80.60
ATOM     16  CG2 THR     2       6.526 -15.019   2.864  1.00 83.46
ATOM     17  N   VAL     3       6.308 -12.396  -0.278  1.00 50.70
ATOM     18  CA  VAL     3       5.190 -12.030  -1.187  1.00 45.60
ATOM     19  C   VAL     3       3.954 -12.870  -0.844  1.00 59.70
ATOM     20  O   VAL     3       2.834 -12.471  -1.090  1.00 47.30
ATOM     21  CB  VAL     3       5.608 -12.274  -2.641  1.00 44.00
ATOM     22  CG1 VAL     3       5.542 -13.771  -2.959  1.00 30.70
ATOM     23  CG2 VAL     3       4.664 -11.514  -3.573  1.00 40.35
ATOM     24  N   GLU     4       4.146 -14.029  -0.272  1.00 80.70
ATOM     25  CA  GLU     4       2.976 -14.882   0.086  1.00 83.60
ATOM     26  C   GLU     4       2.153 -14.190   1.175  1.00 80.50
ATOM     27  O   GLU     4       0.942 -14.141   1.109  1.00 85.40
ATOM     28  CB  GLU     4       3.465 -16.238   0.597  1.00 87.55
ATOM     29  CG  GLU     4       2.336 -17.264   0.479  1.00 81.20
ATOM     30  CD  GLU     4       2.929 -18.671   0.391  1.00 70.10
ATOM     31  OE1 GLU     4       4.056 -18.846   0.823  1.00 77.75
ATOM     32  OE2 GLU     4       2.246 -19.551  -0.108  1.00 80.90
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 
STOICH A2B2
PARENT N/A
ATOM      1  N   ALA A   2      66.410  61.318   7.312  1.00 80.56           N  
ATOM      2  CA  ALA A   2      67.149  60.105   6.984  1.00 80.55           C  
ATOM      3  C   ALA A   2      66.481  58.861   7.568  1.00 80.24           C  
ATOM      4  O   ALA A   2      66.323  57.855   6.871  1.00 80.19           O  
ATOM      5  CB  ALA A   2      68.602  60.207   7.448  1.00 80.18           C  
ATOM      6  N   ARG A   3      66.088  58.921   8.836  1.00 50.80           N  
ATOM      7  CA  ARG A   3      65.379  57.793   9.441  1.00 50.96           C  
ATOM      8  C   ARG A   3      63.851  57.931   9.360  1.00 50.56           C  
ATOM      9  O   ARG A   3      63.225  58.629  10.165  1.00 50.84           O  
ATOM     10  CB  ARG A   3      65.832  57.564  10.878  1.00 50.52           C  
ATOM     11  CG  ARG A   3      67.276  57.122  11.014  1.00 50.18           C  
ATOM     12  CD  ARG A   3      67.694  57.037  12.485  1.00 50.62           C  
ATOM     13  NE  ARG A   3      67.073  55.906  13.171  1.00 50.65           N  
ATOM     14  CZ  ARG A   3      67.192  55.663  14.473  1.00 50.45           C  
ATOM     15  NH1 ARG A   3      67.898  56.480  15.241  1.00 50.61           N  
ATOM     16  NH2 ARG A   3      66.596  54.608  15.011  1.00 50.01           N  
ATOM     17  N   ILE A   4      63.261  57.272   8.370  1.00 80.59           N  
ATOM     18  CA  ILE A   4      61.810  57.250   8.216  1.00 80.32           C  
ATOM     19  C   ILE A   4      61.262  56.084   9.014  1.00 80.36           C  
ATOM     20  O   ILE A   4      61.515  54.920   8.685  1.00 80.81           O  
ATOM     21  CB  ILE A   4      61.418  57.061   6.750  1.00 80.05           C  
ATOM     22  CG1 ILE A   4      61.958  58.216   5.903  1.00 80.45           C  
ATOM     23  CG2 ILE A   4      59.899  56.935   6.606  1.00 80.20           C  
ATOM     24  CD1 ILE A   4      61.682  58.059   4.405  1.00 80.87           C  
TER
PARENT 1abc
ATOM    577  N   GLN B   1      28.350  17.252   8.838  1.00 70.30           N  
ATOM    578  CA  GLN B   1      28.340  18.142   7.644  1.00 70.24           C  
ATOM    579  C   GLN B   1      28.765  19.556   8.023  1.00 70.61           C  
ATOM    580  O   GLN B   1      28.866  19.893   9.209  1.00 70.62           O  
ATOM    581  CB  GLN B   1      26.941  18.176   7.013  1.00 70.82           C  
ATOM    582  CG  GLN B   1      26.851  19.045   5.768  1.00 70.64           C  
ATOM    583  CD  GLN B   1      26.103  18.370   4.654  1.00 70.30           C  
ATOM    584  OE1 GLN B   1      26.147  17.151   4.527  1.00 70.37           O  
ATOM    585  NE2 GLN B   1      25.426  19.152   3.825  1.00 70.67           N  
ATOM    586  N   LYS B   2      29.007  20.382   7.007  1.00 50.53           N  
ATOM    587  CA  LYS B   2      29.423  21.760   7.223  1.00 50.08           C  
ATOM    588  C   LYS B   2      28.253  22.741   7.066  1.00 50.20           C  
ATOM    589  O   LYS B   2      27.489  22.695   6.100  1.00 50.51           O  
ATOM    590  CB  LYS B   2      30.561  22.104   6.264  1.00 50.06           C  
ATOM    591  CG  LYS B   2      31.277  23.381   6.592  1.00 50.24           C  
ATOM    592  CD  LYS B   2      32.723  23.323   6.153  1.00 50.30           C  
ATOM    593  CE  LYS B   2      33.560  22.551   7.144  1.00 50.91           C  
ATOM    594  NZ  LYS B   2      34.976  23.004   7.075  1.00 50.63           N  
ATOM    595  N   THR B   3      28.120  23.623   8.047  1.00 70.04           N  
ATOM    596  CA  THR B   3      27.054  24.606   8.062  1.00 70.76           C  
ATOM    597  C   THR B   3      27.306  25.741   7.072  1.00 70.84           C  
ATOM    598  O   THR B   3      28.422  25.912   6.574  1.00 70.53           O  
ATOM    599  CB  THR B   3      26.897  25.215   9.469  1.00 70.71           C  
ATOM    600  OG1 THR B   3      28.028  26.045   9.770  1.00 70.75           O  
ATOM    601  CG2 THR B   3      26.807  24.118  10.507  1.00 70.32           C 
TER
ATOM     70  N   ALA C   2      17.139  38.489   7.542  1.00 80.40           N  
ATOM     71  CA  ALA C   2      16.401  39.708   7.233  1.00 80.49           C  
ATOM     72  C   ALA C   2      17.081  40.939   7.824  1.00 80.51           C  
ATOM     73  O   ALA C   2      17.221  41.955   7.138  1.00 80.84           O  
ATOM     74  CB  ALA C   2      14.954  39.610   7.712  1.00 80.41           C  
ATOM     75  N   ARG C   3      17.504  40.862   9.087  1.00 40.11           N  
ATOM     76  CA  ARG C   3      18.215  41.993   9.686  1.00 40.09           C  
ATOM     77  C   ARG C   3      19.746  41.845   9.588  1.00 40.10           C  
ATOM     78  O   ARG C   3      20.379  41.144  10.389  1.00 40.06           O  
ATOM     79  CB  ARG C   3      17.779  42.223  11.128  1.00 40.49           C  
ATOM     80  CG  ARG C   3      16.326  42.657  11.272  1.00 40.72           C  
ATOM     81  CD  ARG C   3      15.905  42.771  12.734  1.00 40.86           C  
ATOM     82  NE  ARG C   3      16.538  43.899  13.407  1.00 40.46           N  
ATOM     83  CZ  ARG C   3      16.460  44.127  14.712  1.00 40.48           C  
ATOM     84  NH1 ARG C   3      15.783  43.294  15.485  1.00 40.75           N  
ATOM     85  NH2 ARG C   3      17.057  45.186  15.239  1.00 40.68           N  
ATOM     86  N   ILE C   4      20.329  42.493   8.586  1.00 80.62           N  
ATOM     87  CA  ILE C   4      21.772  42.515   8.415  1.00 80.68           C  
ATOM     88  C   ILE C   4      22.324  43.671   9.214  1.00 80.12           C  
ATOM     89  O   ILE C   4      22.056  44.830   8.893  1.00 80.89           O  
ATOM     90  CB  ILE C   4      22.151  42.705   6.945  1.00 80.69           C  
ATOM     91  CG1 ILE C   4      21.583  41.559   6.110  1.00 80.63           C  
ATOM     92  CG2 ILE C   4      23.672  42.799   6.774  1.00 80.94           C  
ATOM     93  CD1 ILE C   4      21.832  41.708   4.619  1.00 80.50           C  
TER
ATOM   2076  N   GLN D   1      -5.202 -31.148  19.518  1.00 60.90           N  
ATOM   2077  CA  GLN D   1      -4.657 -29.990  20.288  1.00 60.01           C  
ATOM   2078  C   GLN D   1      -3.890 -30.442  21.508  1.00 60.88           C  
ATOM   2079  O   GLN D   1      -3.784 -29.715  22.500  1.00 60.19           O  
ATOM   2080  CB  GLN D   1      -5.777 -29.086  20.761  1.00 60.28           C  
ATOM   2081  CG  GLN D   1      -5.605 -27.661  20.342  1.00 60.13           C  
ATOM   2082  CD  GLN D   1      -6.792 -27.230  19.563  1.00 60.49           C  
ATOM   2083  OE1 GLN D   1      -7.914 -27.444  20.008  1.00 60.58           O  
ATOM   2084  NE2 GLN D   1      -6.574 -26.639  18.389  1.00 60.22           N  
ATOM   2085  N   LYS D   2      -3.368 -31.653  21.440  1.00 30.19           N  
ATOM   2086  CA  LYS D   2      -2.612 -32.197  22.545  1.00 30.61           C  
ATOM   2087  C   LYS D   2      -1.686 -33.248  21.993  1.00 30.53           C  
ATOM   2088  O   LYS D   2      -2.009 -33.946  21.031  1.00 30.89           O  
ATOM   2089  CB  LYS D   2      -3.545 -32.831  23.588  1.00 30.00           C  
ATOM   2090  CG  LYS D   2      -4.381 -31.846  24.404  1.00 30.19           C  
ATOM   2091  CD  LYS D   2      -5.747 -32.442  24.727  1.00 30.42           C  
ATOM   2092  CE  LYS D   2      -6.619 -31.499  25.543  1.00 30.82           C  
ATOM   2093  NZ  LYS D   2      -6.281 -31.538  26.993  1.00 30.55           N  
ATOM   2094  N   THR D   3      -0.512 -33.331  22.592  1.00 60.45           N  
ATOM   2095  CA  THR D   3       0.451 -34.328  22.187  1.00 60.41           C  
ATOM   2096  C   THR D   3      -0.247 -35.666  22.381  1.00 60.63           C  
ATOM   2097  O   THR D   3      -1.086 -35.814  23.270  1.00 60.24           O  
ATOM   2098  CB  THR D   3       1.689 -34.276  23.070  1.00 60.49           C  
ATOM   2099  OG1 THR D   3       2.475 -33.141  22.697  1.00 60.74           O  
ATOM   2100  CG2 THR D   3       2.505 -35.558  22.932  1.00 60.93           C 
TER
END


Example 3. RNA structure

PFRMAT TS
TARGET R0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1
PARENT N/A
ATOM    845  OP1   G 0   1      -7.077  -0.231 -13.826  1.00 70.00           O
ATOM    846  OP2   G 0   1      -4.765  -1.076 -13.098  1.00 70.00           O
ATOM    847  O5'   G 0   1      -5.886  -1.981 -15.135  1.00 70.00           O
ATOM    848  C5'   G 0   1      -6.709  -1.918 -16.298  1.00 70.00           C
ATOM    849  C4'   G 0   1      -6.322  -3.006 -17.271  1.00 70.00           C
ATOM    850  O4'   G 0   1      -4.936  -2.810 -17.669  1.00 70.00           O
ATOM    851  C3'   G 0   1      -6.371  -4.421 -16.711  1.00 70.00           C
ATOM    852  O3'   G 0   1      -7.670  -4.989 -16.845  1.00 70.00           O
ATOM    853  C2'   G 0   1      -5.326  -5.146 -17.550  1.00 70.00           C
ATOM    854  O2'   G 0   1      -5.835  -5.471 -18.831  1.00 70.00           O
ATOM    855  C1'   G 0   1      -4.266  -4.057 -17.703  1.00 70.00           C
ATOM    856  N9    G 0   1      -3.258  -4.064 -16.647  1.00 70.00           N
ATOM    857  C8    G 0   1      -3.367  -3.513 -15.394  1.00 70.00           C
ATOM    858  N7    G 0   1      -2.300  -3.679 -14.662  1.00 70.00           N
ATOM    859  C5    G 0   1      -1.430  -4.385 -15.483  1.00 70.00           C
ATOM    860  C6    G 0   1      -0.113  -4.857 -15.240  1.00 70.00           C
ATOM    861  O6    G 0   1       0.571  -4.743 -14.217  1.00 70.00           O
ATOM    862  N1    G 0   1       0.402  -5.524 -16.345  1.00 70.00           N
ATOM    863  C2    G 0   1      -0.260  -5.714 -17.530  1.00 70.00           C
ATOM    864  N2    G 0   1       0.405  -6.385 -18.475  1.00 70.00           N
ATOM    865  N3    G 0   1      -1.484  -5.281 -17.772  1.00 70.00           N
ATOM    866  C4    G 0   1      -2.006  -4.630 -16.712  1.00 70.00           C
ATOM    867  P     U 0   2      -8.176  -6.087 -15.783  1.00 80.00           P
ATOM    868  OP1   U 0   2      -7.261  -7.253 -15.890  1.00 80.00           O
ATOM    869  OP2   U 0   2      -9.636  -6.279 -15.978  1.00 80.00           O
ATOM    870  O5'   U 0   2      -7.936  -5.396 -14.366  1.00 80.00           O
ATOM    871  C5'   U 0   2      -8.944  -5.423 -13.354  1.00 80.00           C
ATOM    872  C4'   U 0   2      -8.313  -5.364 -11.981  1.00 80.00           C
ATOM    873  O4'   U 0   2      -7.113  -6.190 -11.983  1.00 80.00           O
ATOM    874  C3'   U 0   2      -7.861  -3.976 -11.530  1.00 80.00           C
ATOM    875  O3'   U 0   2      -8.105  -3.794 -10.136  1.00 80.00           O
ATOM    876  C2'   U 0   2      -6.374  -3.969 -11.873  1.00 80.00           C
ATOM    877  O2'   U 0   2      -5.641  -3.123 -11.006  1.00 80.00           O
ATOM    878  C1'   U 0   2      -6.006  -5.417 -11.571  1.00 80.00           C
ATOM    879  N1    U 0   2      -4.810  -5.906 -12.273  1.00 80.00           N
ATOM    880  C2    U 0   2      -3.697  -6.214 -11.512  1.00 80.00           C
ATOM    881  O2    U 0   2      -3.667  -6.091 -10.301  1.00 80.00           O
ATOM    882  N3    U 0   2      -2.618  -6.672 -12.223  1.00 80.00           N
ATOM    883  C4    U 0   2      -2.537  -6.850 -13.584  1.00 80.00           C
ATOM    884  O4    U 0   2      -1.495  -7.280 -14.077  1.00 80.00           O
ATOM    885  C5    U 0   2      -3.725  -6.506 -14.300  1.00 80.00           C
ATOM    886  C6    U 0   2      -4.798  -6.057 -13.640  1.00 80.00           C
ATOM    887  P     G 0   3      -8.106  -2.312  -9.507  1.00 70.00           P
ATOM    888  OP1   G 0   3      -7.806  -1.347 -10.597  1.00 70.00           O
ATOM    889  OP2   G 0   3      -7.257  -2.327  -8.289  1.00 70.00           O
ATOM    890  O5'   G 0   3      -9.617  -2.089  -9.050  1.00 70.00           O
ATOM    891  C5'   G 0   3     -10.568  -1.481  -9.923  1.00 70.00           C
ATOM    892  C4'   G 0   3     -11.972  -1.717  -9.415  1.00 70.00           C
ATOM    893  O4'   G 0   3     -12.150  -3.138  -9.157  1.00 70.00           O
ATOM    894  C3'   G 0   3     -12.316  -1.039  -8.095  1.00 70.00           C
ATOM    895  O3'   G 0   3     -12.776   0.296  -8.297  1.00 70.00           O
ATOM    896  C2'   G 0   3     -13.400  -1.949  -7.532  1.00 70.00           C
ATOM    897  O2'   G 0   3     -14.642  -1.718  -8.170  1.00 70.00           O
ATOM    898  C1'   G 0   3     -12.878  -3.321  -7.955  1.00 70.00           C
ATOM    899  N9    G 0   3     -11.995  -3.946  -6.974  1.00 70.00           N
ATOM    900  C8    G 0   3     -10.630  -4.076  -7.053  1.00 70.00           C
ATOM    901  N7    G 0   3     -10.109  -4.683  -6.022  1.00 70.00           N
ATOM    902  C5    G 0   3     -11.198  -4.973  -5.210  1.00 70.00           C
ATOM    903  C6    G 0   3     -11.260  -5.628  -3.952  1.00 70.00           C
ATOM    904  O6    G 0   3     -10.334  -6.100  -3.279  1.00 70.00           O
ATOM    905  N1    G 0   3     -12.565  -5.710  -3.483  1.00 70.00           N
ATOM    906  C2    G 0   3     -13.669  -5.226  -4.136  1.00 70.00           C
ATOM    907  N2    G 0   3     -14.840  -5.400  -3.517  1.00 70.00           N
ATOM    908  N3    G 0   3     -13.629  -4.616  -5.307  1.00 70.00           N
ATOM    909  C4    G 0   3     -12.370  -4.524  -5.784  1.00 70.00           C
TER
ATOM    910  P     G 1   1     -12.645   1.375  -7.111  1.00 80.00           P
ATOM    911  OP1   G 1   1     -13.262   2.636  -7.597  1.00 80.00           O
ATOM    912  OP2   G 1   1     -11.239   1.385  -6.633  1.00 80.00           O
ATOM    913  O5'   G 1   1     -13.567   0.790  -5.950  1.00 80.00           O
ATOM    914  C5'   G 1   1     -14.989   0.808  -6.064  1.00 80.00           C
ATOM    915  C4'   G 1   1     -15.620   0.149  -4.860  1.00 80.00           C
ATOM    916  O4'   G 1   1     -15.122  -1.208  -4.730  1.00 80.00           O
ATOM    917  C3'   G 1   1     -15.289   0.769  -3.511  1.00 80.00           C
ATOM    918  O3'   G 1   1     -16.074   1.930  -3.251  1.00 80.00           O
ATOM    919  C2'   G 1   1     -15.600  -0.373  -2.550  1.00 80.00           C
ATOM    920  O2'   G 1   1     -16.993  -0.482  -2.322  1.00 80.00           O
ATOM    921  C1'   G 1   1     -15.141  -1.586  -3.364  1.00 80.00           C
ATOM    922  N9    G 1   1     -13.811  -2.059  -2.992  1.00 80.00           N
ATOM    923  C8    G 1   1     -12.657  -1.974  -3.733  1.00 80.00           C
ATOM    924  N7    G 1   1     -11.620  -2.488  -3.131  1.00 80.00           N
ATOM    925  C5    G 1   1     -12.119  -2.941  -1.917  1.00 80.00           C
ATOM    926  C6    G 1   1     -11.466  -3.591  -0.836  1.00 80.00           C
ATOM    927  O6    G 1   1     -10.276  -3.911  -0.731  1.00 80.00           O
ATOM    928  N1    G 1   1     -12.350  -3.872   0.199  1.00 80.00           N
ATOM    929  C2    G 1   1     -13.687  -3.569   0.199  1.00 80.00           C
ATOM    930  N2    G 1   1     -14.370  -3.919   1.290  1.00 80.00           N
ATOM    931  N3    G 1   1     -14.308  -2.966  -0.798  1.00 80.00           N
ATOM    932  C4    G 1   1     -13.470  -2.682  -1.816  1.00 80.00           C
ATOM    933  P     A 1   2     -15.537   3.045  -2.223  1.00 50.50           P
ATOM    934  OP1   A 1   2     -16.462   4.203  -2.309  1.00 50.50           O
ATOM    935  OP2   A 1   2     -14.085   3.247  -2.464  1.00 50.50           O
ATOM    936  O5'   A 1   2     -15.716   2.369  -0.791  1.00 50.50           O
ATOM    937  C5'   A 1   2     -17.013   2.151  -0.238  1.00 50.50           C
ATOM    938  C4'   A 1   2     -16.904   1.791   1.226  1.00 50.50           C
ATOM    939  O4'   A 1   2     -16.439   0.417   1.339  1.00 50.50           O
ATOM    940  C3'   A 1   2     -15.898   2.603   2.032  1.00 50.50           C
ATOM    941  O3'   A 1   2     -16.464   3.816   2.521  1.00 50.50           O
ATOM    942  C2'   A 1   2     -15.526   1.640   3.151  1.00 50.50           C
ATOM    943  O2'   A 1   2     -16.539   1.573   4.137  1.00 50.50           O
ATOM    944  C1'   A 1   2     -15.494   0.317   2.390  1.00 50.50           C
ATOM    945  N9    A 1   2     -14.187   0.012   1.809  1.00 50.50           N
ATOM    946  C8    A 1   2     -13.738   0.315   0.547  1.00 50.50           C
ATOM    947  N7    A 1   2     -12.511  -0.083   0.314  1.00 50.50           N
ATOM    948  C5    A 1   2     -12.125  -0.688   1.503  1.00 50.50           C
ATOM    949  C6    A 1   2     -10.931  -1.310   1.904  1.00 50.50           C
ATOM    950  N6    A 1   2      -9.860  -1.433   1.120  1.00 50.50           N
ATOM    951  N1    A 1   2     -10.874  -1.809   3.157  1.00 50.50           N
ATOM    952  C2    A 1   2     -11.949  -1.687   3.946  1.00 50.50           C
ATOM    953  N3    A 1   2     -13.126  -1.124   3.684  1.00 50.50           N
ATOM    954  C4    A 1   2     -13.149  -0.638   2.431  1.00 50.50           C
ATOM    955  P     G 1   3     -15.512   5.081   2.810  1.00 80.00           P
ATOM    956  OP1   G 1   3     -16.374   6.170   3.338  1.00 80.00           O
ATOM    957  OP2   G 1   3     -14.679   5.325   1.604  1.00 80.00           O
ATOM    958  O5'   G 1   3     -14.555   4.587   3.986  1.00 80.00           O
ATOM    959  C5'   G 1   3     -14.929   4.745   5.355  1.00 80.00           C
ATOM    960  C4'   G 1   3     -14.303   3.658   6.201  1.00 80.00           C
ATOM    961  O4'   G 1   3     -13.959   2.527   5.358  1.00 80.00           O
ATOM    962  C3'   G 1   3     -12.989   4.024   6.874  1.00 80.00           C
ATOM    963  O3'   G 1   3     -13.208   4.736   8.089  1.00 80.00           O
ATOM    964  C2'   G 1   3     -12.344   2.661   7.108  1.00 80.00           C
ATOM    965  O2'   G 1   3     -12.878   2.038   8.262  1.00 80.00           O
ATOM    966  C1'   G 1   3     -12.808   1.883   5.874  1.00 80.00           C
ATOM    967  N9    G 1   3     -11.806   1.812   4.814  1.00 80.00           N
ATOM    968  C8    G 1   3     -11.929   2.263   3.522  1.00 80.00           C
ATOM    969  N7    G 1   3     -10.863   2.053   2.800  1.00 80.00           N
ATOM    970  C5    G 1   3      -9.979   1.427   3.668  1.00 80.00           C
ATOM    971  C6    G 1   3      -8.656   0.958   3.456  1.00 80.00           C
ATOM    972  O6    G 1   3      -7.979   1.001   2.423  1.00 80.00           O
ATOM    973  N1    G 1   3      -8.124   0.390   4.608  1.00 80.00           N
ATOM    974  C2    G 1   3      -8.777   0.285   5.808  1.00 80.00           C
ATOM    975  N2    G 1   3      -8.095  -0.293   6.800  1.00 80.00           N
ATOM    976  N3    G 1   3     -10.008   0.716   6.022  1.00 80.00           N
ATOM    977  C4    G 1   3     -10.545   1.272   4.916  1.00 80.00           C
TER
END


Example 4. Protein-RNA complex

PFRMAT TS
TARGET A0999
AUTHOR 1234-5678-9000
REMARK Predictor remarks
METHOD Description of methods used
METHOD Description of methods used
MODEL  1
PARENT N/A
ATOM    577  N   GLN A   1      28.350  17.252   8.838  1.00 38.30           N  
ATOM    578  CA  GLN A   1      28.340  18.142   7.644  1.00 36.24           C  
ATOM    579  C   GLN A   1      28.765  19.556   8.023  1.00 35.61           C  
ATOM    580  O   GLN A   1      28.866  19.893   9.209  1.00 36.62           O  
ATOM    581  CB  GLN A   1      26.941  18.176   7.013  1.00 36.82           C  
ATOM    582  CG  GLN A   1      26.851  19.045   5.768  1.00 36.64           C  
ATOM    583  CD  GLN A   1      26.103  18.370   4.654  1.00 38.30           C  
ATOM    584  OE1 GLN A   1      26.147  17.151   4.527  1.00 31.37           O  
ATOM    585  NE2 GLN A   1      25.426  19.152   3.825  1.00 38.67           N  
ATOM    586  N   LYS A   2      29.007  20.382   7.007  1.00 33.53           N  
ATOM    587  CA  LYS A   2      29.423  21.760   7.223  1.00 30.08           C  
ATOM    588  C   LYS A   2      28.253  22.741   7.066  1.00 37.20           C  
ATOM    589  O   LYS A   2      27.489  22.695   6.100  1.00 36.51           O  
ATOM    590  CB  LYS A   2      30.561  22.104   6.264  1.00 33.06           C  
ATOM    591  CG  LYS A   2      31.277  23.381   6.592  1.00 34.24           C  
ATOM    592  CD  LYS A   2      32.723  23.323   6.153  1.00 37.30           C  
ATOM    593  CE  LYS A   2      33.560  22.551   7.144  1.00 38.91           C  
ATOM    594  NZ  LYS A   2      34.976  23.004   7.075  1.00 30.63           N  
ATOM    595  N   THR A   3      28.120  23.623   8.047  1.00 33.04           N  
ATOM    596  CA  THR A   3      27.054  24.606   8.062  1.00 30.76           C  
ATOM    597  C   THR A   3      27.306  25.741   7.072  1.00 38.84           C  
ATOM    598  O   THR A   3      28.422  25.912   6.574  1.00 38.53           O  
ATOM    599  CB  THR A   3      26.897  25.215   9.469  1.00 31.71           C  
ATOM    600  OG1 THR A   3      28.028  26.045   9.770  1.00 32.75           O  
ATOM    601  CG2 THR A   3      26.807  24.118  10.507  1.00 38.32           C 
TER
ATOM     70  N   ALA B   2      17.139  38.489   7.542  1.00 84.40           N  
ATOM     71  CA  ALA B   2      16.401  39.708   7.233  1.00 82.49           C  
ATOM     72  C   ALA B   2      17.081  40.939   7.824  1.00 88.51           C  
ATOM     73  O   ALA B   2      17.221  41.955   7.138  1.00 82.84           O  
ATOM     74  CB  ALA B   2      14.954  39.610   7.712  1.00 80.41           C  
ATOM     75  N   ARG B   3      17.504  40.862   9.087  1.00 83.11           N  
ATOM     76  CA  ARG B   3      18.215  41.993   9.686  1.00 80.09           C  
ATOM     77  C   ARG B   3      19.746  41.845   9.588  1.00 86.10           C  
ATOM     78  O   ARG B   3      20.379  41.144  10.389  1.00 85.06           O  
ATOM     79  CB  ARG B   3      17.779  42.223  11.128  1.00 80.49           C  
ATOM     80  CG  ARG B   3      16.326  42.657  11.272  1.00 86.72           C  
ATOM     81  CD  ARG B   3      15.905  42.771  12.734  1.00 84.86           C  
ATOM     82  NE  ARG B   3      16.538  43.899  13.407  1.00 84.46           N  
ATOM     83  CZ  ARG B   3      16.460  44.127  14.712  1.00 85.48           C  
ATOM     84  NH1 ARG B   3      15.783  43.294  15.485  1.00 84.75           N  
ATOM     85  NH2 ARG B   3      17.057  45.186  15.239  1.00 89.68           N  
ATOM     86  N   ILE B   4      20.329  42.493   8.586  1.00 81.62           N  
ATOM     87  CA  ILE B   4      21.772  42.515   8.415  1.00 88.68           C  
ATOM     88  C   ILE B   4      22.324  43.671   9.214  1.00 84.12           C  
ATOM     89  O   ILE B   4      22.056  44.830   8.893  1.00 87.89           O  
ATOM     90  CB  ILE B   4      22.151  42.705   6.945  1.00 83.69           C  
ATOM     91  CG1 ILE B   4      21.583  41.559   6.110  1.00 84.63           C  
ATOM     92  CG2 ILE B   4      23.672  42.799   6.774  1.00 80.94           C  
ATOM     93  CD1 ILE B   4      21.832  41.708   4.619  1.00 85.50           C  
TER
ATOM   2076  N   GLN C   1      -5.202 -31.148  19.518  1.00 77.90           N  
ATOM   2077  CA  GLN C   1      -4.657 -29.990  20.288  1.00 78.01           C  
ATOM   2078  C   GLN C   1      -3.890 -30.442  21.508  1.00 76.88           C  
ATOM   2079  O   GLN C   1      -3.784 -29.715  22.500  1.00 77.19           O  
ATOM   2080  CB  GLN C   1      -5.777 -29.086  20.761  1.00 79.28           C  
ATOM   2081  CG  GLN C   1      -5.605 -27.661  20.342  1.00 71.13           C  
ATOM   2082  CD  GLN C   1      -6.792 -27.230  19.563  1.00 72.49           C  
ATOM   2083  OE1 GLN C   1      -7.914 -27.444  20.008  1.00 73.58           O  
ATOM   2084  NE2 GLN C   1      -6.574 -26.639  18.389  1.00 73.22           N  
ATOM   2085  N   LYS C   2      -3.368 -31.653  21.440  1.00 75.19           N  
ATOM   2086  CA  LYS C   2      -2.612 -32.197  22.545  1.00 73.61           C  
ATOM   2087  C   LYS C   2      -1.686 -33.248  21.993  1.00 71.53           C  
ATOM   2088  O   LYS C   2      -2.009 -33.946  21.031  1.00 71.89           O  
ATOM   2089  CB  LYS C   2      -3.545 -32.831  23.588  1.00 74.00           C  
ATOM   2090  CG  LYS C   2      -4.381 -31.846  24.404  1.00 74.19           C  
ATOM   2091  CD  LYS C   2      -5.747 -32.442  24.727  1.00 75.42           C  
ATOM   2092  CE  LYS C   2      -6.619 -31.499  25.543  1.00 75.82           C  
ATOM   2093  NZ  LYS C   2      -6.281 -31.538  26.993  1.00 75.55           N  
ATOM   2094  N   THR C   3      -0.512 -33.331  22.592  1.00 79.45           N  
ATOM   2095  CA  THR C   3       0.451 -34.328  22.187  1.00 77.41           C  
ATOM   2096  C   THR C   3      -0.247 -35.666  22.381  1.00 76.63           C  
ATOM   2097  O   THR C   3      -1.086 -35.814  23.270  1.00 76.24           O  
ATOM   2098  CB  THR C   3       1.689 -34.276  23.070  1.00 76.49           C  
ATOM   2099  OG1 THR C   3       2.475 -33.141  22.697  1.00 75.74           O  
ATOM   2100  CG2 THR C   3       2.505 -35.558  22.932  1.00 75.93           C 
TER
ATOM      1  P     G 0   1      -0.520   0.293  -2.149  1.00 11.89           P
ATOM      2  OP1   G 0   1      -0.096  -0.880  -2.952  1.00 14.35           O
ATOM      3  OP2   G 0   1      -1.943   0.655  -2.048  1.00 12.68           O
ATOM      4  O5'   G 0   1       0.012   0.179  -0.658  1.00 10.34           O
ATOM      5  C5'   G 0   1       1.425  -0.140  -0.414  1.00 40.00           C
ATOM      6  C4'   G 0   1       1.652  -0.059   1.077  1.00 40.00           C
ATOM      7  O4'   G 0   1       1.483   1.323   1.502  1.00 40.00           O
ATOM      8  C3'   G 0   1       0.670  -0.857   1.928  1.00 40.00           C
ATOM      9  O3'   G 0   1       1.119  -2.195   2.125  1.00 40.00           O
ATOM     10  C2'   G 0   1       0.631  -0.058   3.224  1.00 40.00           C
ATOM     11  O2'   G 0   1       1.777  -0.309   4.016  1.00 40.00           O
ATOM     12  C1'   G 0   1       0.707   1.369   2.686  1.00 40.00           C
ATOM     13  N9    G 0   1      -0.595   1.945   2.360  1.00 40.00           N
ATOM     14  C8    G 0   1      -0.999   2.449   1.148  1.00 40.00           C
ATOM     15  N7    G 0   1      -2.227   2.891   1.157  1.00 40.00           N
ATOM     16  C5    G 0   1      -2.660   2.667   2.458  1.00 40.00           C
ATOM     17  C6    G 0   1      -3.910   2.942   3.072  1.00 40.00           C
ATOM     18  O6    G 0   1      -4.921   3.452   2.573  1.00 40.00           O
ATOM     19  N1    G 0   1      -3.919   2.556   4.407  1.00 40.00           N
ATOM     20  C2    G 0   1      -2.864   1.980   5.067  1.00 40.00           C
ATOM     21  N2    G 0   1      -3.068   1.679   6.352  1.00 40.00           N
ATOM     22  N3    G 0   1      -1.696   1.719   4.510  1.00 40.00           N
ATOM     23  C4    G 0   1      -1.663   2.086   3.213  1.00 40.00           C
ATOM     24  P     C 0   2       0.081  -3.417   1.982  1.00 70.30           P
ATOM     25  OP1   C 0   2       0.874  -4.672   1.982  1.00 70.30           O
ATOM     26  OP2   C 0   2      -0.835  -3.128   0.849  1.00 70.30           O
ATOM     27  O5'   C 0   2      -0.766  -3.362   3.330  1.00 70.30           O
ATOM     28  C5'   C 0   2      -0.145  -3.573   4.598  1.00 70.30           C
ATOM     29  C4'   C 0   2      -1.121  -3.275   5.712  1.00 70.30           C
ATOM     30  O4'   C 0   2      -1.478  -1.866   5.658  1.00 70.30           O
ATOM     31  C3'   C 0   2      -2.449  -4.016   5.632  1.00 70.30           C
ATOM     32  O3'   C 0   2      -2.375  -5.296   6.256  1.00 70.30           O
ATOM     33  C2'   C 0   2      -3.398  -3.071   6.358  1.00 70.00           C
ATOM     34  O2'   C 0   2      -3.249  -3.172   7.762  1.00 70.00           O
ATOM     35  C1'   C 0   2      -2.865  -1.713   5.906  1.00 70.00           C
ATOM     36  N1    C 0   2      -3.504  -1.202   4.681  1.00 70.00           N
ATOM     37  C2    C 0   2      -4.815  -0.721   4.753  1.00 70.00           C
ATOM     38  O2    C 0   2      -5.405  -0.742   5.843  1.00 70.00           O
ATOM     39  N3    C 0   2      -5.407  -0.246   3.635  1.00 70.00           N
ATOM     40  C4    C 0   2      -4.741  -0.240   2.480  1.00 70.00           C
ATOM     41  N4    C 0   2      -5.366   0.240   1.406  1.00 70.00           N
ATOM     42  C5    C 0   2      -3.406  -0.726   2.375  1.00 70.00           C
ATOM     43  C6    C 0   2      -2.832  -1.195   3.490  1.00 70.00           C
ATOM     44  P     U 0   3      -3.426  -6.445   5.852  1.00 40.00           P
ATOM     45  OP1   U 0   3      -2.981  -7.702   6.504  1.00 40.00           O
ATOM     46  OP2   U 0   3      -3.622  -6.412   4.380  1.00 40.00           O
ATOM     47  O5'   U 0   3      -4.787  -5.982   6.539  1.00 40.00           O
ATOM     48  C5'   U 0   3      -4.920  -5.945   7.959  1.00 40.00           C
ATOM     49  C4'   U 0   3      -6.375  -5.805   8.344  1.00 40.00           C
ATOM     50  O4'   U 0   3      -6.778  -4.418   8.156  1.00 40.00           O
ATOM     51  C3'   U 0   3      -7.356  -6.613   7.501  1.00 40.00           C
ATOM     52  O3'   U 0   3      -7.531  -7.932   8.010  1.00 40.00           O
ATOM     53  C2'   U 0   3      -8.626  -5.778   7.591  1.00 40.00           C
ATOM     54  O2'   U 0   3      -9.262  -5.944   8.844  1.00 40.00           O
ATOM     55  C1'   U 0   3      -8.042  -4.369   7.518  1.00 40.00           C
ATOM     56  N1    U 0   3      -7.851  -3.876   6.146  1.00 40.00           N
ATOM     57  C2    U 0   3      -8.904  -3.213   5.545  1.00 40.00           C
ATOM     58  O2    U 0   3      -9.971  -3.025   6.099  1.00 40.00           O
ATOM     59  N3    U 0   3      -8.660  -2.778   4.269  1.00 40.00           N
ATOM     60  C4    U 0   3      -7.501  -2.931   3.546  1.00 40.00           C
ATOM     61  O4    U 0   3      -7.437  -2.480   2.403  1.00 40.00           O
ATOM     62  C5    U 0   3      -6.460  -3.627   4.234  1.00 40.00           C
ATOM     63  C6    U 0   3      -6.662  -4.068   5.479  1.00 40.00           C
TER
END


Example 5. Estimates of model accuracy prediction

(A) QMODE1. Global Model Quality Score

PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
METHOD Description of methods used
MODEL 1
QMODE 1
T1031TS000_1o 0.8 0.4
T1031TS999_1o 0.7 X
END
(B) QMODE2. Residue-based Interface Assessment

PFRMAT QA
TARGET T0999
AUTHOR 1234-5678-9000
REMARK Reliability of residues being in Interfaces
METHOD Description of methods used
MODEL 1
QMODE 2
T1031TS000_1o 0.8 0.4 A1:0.9 A3:0.9 A17:0.7 A19:0.7 B45:0.7 B49:0.4
B50:0.4 B53:0.8
T1031TS999_1o 0.7 X A15:0.5 A17:0.9 A44:0.7 A46:0.7 B4:0.3 B9:0.4
END


Example 6.1. Ligand prediction (receptor coordinates and ligand pose)

PFRMAT LG
TARGET T1999
AUTHOR 0123-4567-8901
METHOD LG prediction
METHOD -------------
MODEL 1
REMARK Predictor remarks
PARENT 1abc 
ATOM      1  N   GLU     1      10.982  -9.774   1.377  1.00 90.00
ATOM      2  CA  GLU     1       9.623  -9.833   1.984  1.00 85.50
ATOM      3  C   GLU     1       8.913 -11.104   1.521  1.00 85.50
ATOM      4  O   GLU     1       9.187 -11.630   0.461  1.00 80.00
ATOM      5  CB  GLU     1       8.814  -8.614   1.546  1.00 85.45
ATOM      6  CG  GLU     1       7.372  -8.754   2.039  1.00 75.00
ATOM      7  CD  GLU     1       7.339  -8.625   3.562  1.00 93.50
ATOM      8  OE1 GLU     1       8.370  -8.307   4.131  1.00 90.50
ATOM      9  OE2 GLU     1       6.284  -8.846   4.132  1.00 85.40
ATOM     10  N   THR     2       7.998 -11.599   2.304  1.00 70.60
ATOM     11  CA  THR     2       7.266 -12.832   1.907  1.00 75.60
ATOM     12  C   THR     2       6.096 -12.456   1.005  1.00 76.40
ATOM     13  O   THR     2       5.008 -12.217   1.466  1.00 75.60
ATOM     14  CB  THR     2       6.731 -13.533   3.157  1.00 70.90
ATOM     15  OG1 THR     2       7.662 -13.379   4.220  1.00 80.60
ATOM     16  CG2 THR     2       6.526 -15.019   2.864  1.00 83.46
ATOM     17  N   VAL     3       6.308 -12.396  -0.278  1.00 50.70
ATOM     18  CA  VAL     3       5.190 -12.030  -1.187  1.00 45.60
ATOM     19  C   VAL     3       3.954 -12.870  -0.844  1.00 59.70
ATOM     20  O   VAL     3       2.834 -12.471  -1.090  1.00 47.30
ATOM     21  CB  VAL     3       5.608 -12.274  -2.641  1.00 44.00
ATOM     22  CG1 VAL     3       5.542 -13.771  -2.959  1.00 30.70
ATOM     23  CG2 VAL     3       4.664 -11.514  -3.573  1.00 40.35
ATOM     24  N   GLU     4       4.146 -14.029  -0.272  1.00 80.70
ATOM     25  CA  GLU     4       2.976 -14.882   0.086  1.00 83.60
ATOM     26  C   GLU     4       2.153 -14.190   1.175  1.00 80.50
ATOM     27  O   GLU     4       0.942 -14.141   1.109  1.00 85.40
ATOM     28  CB  GLU     4       3.465 -16.238   0.597  1.00 87.55
ATOM     29  CG  GLU     4       2.336 -17.264   0.479  1.00 81.20
ATOM     30  CD  GLU     4       2.929 -18.671   0.391  1.00 70.10
ATOM     31  OE1 GLU     4       4.056 -18.846   0.823  1.00 77.75
ATOM     32  OE2 GLU     4       2.246 -19.551  -0.108  1.00 80.90
TER
LIGAND 001 LIG
LSCORE 0.82
LIG
     RDKit          3D

 16 17  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7 15  1  0
 15 16  1  0
 16  4  1  0
 14 10  1  0
M  END
LIGAND 002 LIG
LSCORE 0.65
LIG
     RDKit          3D

 16 17  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7 15  1  0
 15 16  1  0
 16  4  1  0
 14 10  1  0
M  END
END
MODEL 2
PARENT N/A
... receptor coordinate section
TER
LIGAND 001 LIG
LSCORE 0.71
... ligand coordinate section
M  END
LIGAND 002 LIG
LSCORE 0.31
... ligand coordinate section
M  END
END

------------------------------

Example 6.2. Ligand prediction (affinity only)

PFRMAT LG
TARGET T1999
AUTHOR 0123-4567-8901
METHOD My affinity method description 
METHOD split into multiple lines 
MODEL  1
AFFNTY 1.0 ra
END
MODEL  2
AFFNTY 0.9 ra
END

------------------------------

Example 6.3. Ligand prediction (receptor coordinates, ligand pose and affinity)

PFRMAT LG
TARGET T1999
AUTHOR 0123-4567-8901
METHOD LG prediction
METHOD -------------
MODEL 1
REMARK Predictor remarks
PARENT 1abc 
ATOM      1  N   GLU     1      10.982  -9.774   1.377  1.00 90.00
ATOM      2  CA  GLU     1       9.623  -9.833   1.984  1.00 85.50
ATOM      3  C   GLU     1       8.913 -11.104   1.521  1.00 85.50
ATOM      4  O   GLU     1       9.187 -11.630   0.461  1.00 80.00
ATOM      5  CB  GLU     1       8.814  -8.614   1.546  1.00 85.45
ATOM      6  CG  GLU     1       7.372  -8.754   2.039  1.00 75.00
ATOM      7  CD  GLU     1       7.339  -8.625   3.562  1.00 93.50
ATOM      8  OE1 GLU     1       8.370  -8.307   4.131  1.00 90.50
ATOM      9  OE2 GLU     1       6.284  -8.846   4.132  1.00 85.40
ATOM     10  N   THR     2       7.998 -11.599   2.304  1.00 70.60
ATOM     11  CA  THR     2       7.266 -12.832   1.907  1.00 75.60
ATOM     12  C   THR     2       6.096 -12.456   1.005  1.00 76.40
ATOM     13  O   THR     2       5.008 -12.217   1.466  1.00 75.60
ATOM     14  CB  THR     2       6.731 -13.533   3.157  1.00 70.90
ATOM     15  OG1 THR     2       7.662 -13.379   4.220  1.00 80.60
ATOM     16  CG2 THR     2       6.526 -15.019   2.864  1.00 83.46
ATOM     17  N   VAL     3       6.308 -12.396  -0.278  1.00 50.70
ATOM     18  CA  VAL     3       5.190 -12.030  -1.187  1.00 45.60
ATOM     19  C   VAL     3       3.954 -12.870  -0.844  1.00 59.70
ATOM     20  O   VAL     3       2.834 -12.471  -1.090  1.00 47.30
ATOM     21  CB  VAL     3       5.608 -12.274  -2.641  1.00 44.00
ATOM     22  CG1 VAL     3       5.542 -13.771  -2.959  1.00 30.70
ATOM     23  CG2 VAL     3       4.664 -11.514  -3.573  1.00 40.35
ATOM     24  N   GLU     4       4.146 -14.029  -0.272  1.00 80.70
ATOM     25  CA  GLU     4       2.976 -14.882   0.086  1.00 83.60
ATOM     26  C   GLU     4       2.153 -14.190   1.175  1.00 80.50
ATOM     27  O   GLU     4       0.942 -14.141   1.109  1.00 85.40
ATOM     28  CB  GLU     4       3.465 -16.238   0.597  1.00 87.55
ATOM     29  CG  GLU     4       2.336 -17.264   0.479  1.00 81.20
ATOM     30  CD  GLU     4       2.929 -18.671   0.391  1.00 70.10
ATOM     31  OE1 GLU     4       4.056 -18.846   0.823  1.00 77.75
ATOM     32  OE2 GLU     4       2.246 -19.551  -0.108  1.00 80.90
TER
LIGAND 001 LIG
LSCORE 0.82
LIG
     RDKit          3D

 16 17  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7 15  1  0
 15 16  1  0
 16  4  1  0
 14 10  1  0
M  END
LIGAND 002 LIG
LSCORE 0.65
LIG
     RDKit          3D

 16 17  0  0  0  0  0  0  0  0999 V2000
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
  7 15  1  0
 15 16  1  0
 16  4  1  0
 14 10  1  0
M  END
AFFNTY 0.045 aa
END
MODEL 2
... Data block similar to MODEL 1
END

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