Continuous CASP Model Refinement Experiment
CASPR

Format for Prediction Submission

General rules

Refined models for the CASPR experiment should be submitted as coordinates in the PDB format with adding of several records.

Each submission may contain only one model, beginning with the MODEL record , ending with END, no target residue repetitions.

Submission of a duplicate model (same target, format category, group, model index) will replace previously accepted model, provided it is received before the expiration date.

Each submitted model is automatically verified by the format verification server. Only accepted models will be assigned an ACCESSION CODE. A unique ACCESSION CODE is composed from the number of the target, prediction format category, prediction group number, and model index.

   Examples:

   Accession code  TMR04TS005_1  has the following components:
     TMR04   target number
     TS      abbrev. for Tertiary Structure 
     005     prediction group 5
     1       model index 1

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. Then, after a 'space', please provide the information assossiated with the keyword.

The keyword set is as follows:

TARGET     Target identifier from the CASPR target table
AUTHOR     XXXX-XXXX-XXXX   Registration code of the Group Leader  
REMARK     Comment record (may appear anywhere after the first 2 required lines, optional)
METHOD     Records describing the methods used 
MODEL      Beginning of the data section for the submitted model
END        End of the submitted model

Models should be submitted in Plain Text format, one model per submission.

Record TARGET should appear on the first line of the prediction and is used for all submissions.

Record AUTHOR should specify registration code of the group leader and should appear on the second line of the submission.

Record REMARK is optional and may contain any information modeller want to provide.

Records METHOD are used for all submissions.
These records describe the methods used. Modellers are urged to provide as full a description of the methods as possible, including references, data libraries used, and values of default and non-default parameters. These descriptions will be made available via the Prediction Center WEB pages. Length of 100 - 500 words is suggested.

Record MODEL is used for all submissions to signify the beginning of model data.

   MODEL  n 
     n          Model index n is used to indicate modeller's ranking
                according to her/his belief which model is closest to the 
                target structure (1 <= n <= 5). Model index is included
                automatically in the ACCESSION CODE. All models with index
                higher than 5 will be discarded.

Between the MODEL and END records, protein atomic coordinates should appear in the standard PDB form (80 column long records should be used). Please, put 1.0 in the occupancy field of the PDB record. Error estimates, in Angstroms, when given should be provided in the temperature factor field.

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

Example.

TARGET TMR02
AUTHOR 1232-3454-4565
REMARK Modeller remarks
METHOD Description of methods used
METHOD Description of methods used
METHOD Description of methods used
MODEL  1 
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
END

CASP organizers 01/18/2006

Protein Structure Prediction Center