When you predict protein docking with NovaDock, the first wizard screen is Structures. This screen prompts you to specify structure files to use as the receptor and as the ligand(s) in a docking simulation.

The number of predictions you can submit for folding depends on the type of NovaFold license you have.

  • If you have a term license, the NovaCloud Services view shows the number of predictions that can be run concurrently.
  • If you have one or more individual prediction licenses, the number of predictions you can run concurrently is the same as your total remaining number of purchased predictions. This number can be seen in the NovaCloud Services view.

Note that the ability to submit large numbers of concurrent jobs may fluctuate during peak usage.

To enter the antibody and antigen files, click Enter. The maximum sequence length in both cases is 1,000 residues.

In the Receptor section, use the Browse button to browse to the antigen file in FASTA format. In the Ligand section, use the Browse button to browse to the antibody file in FASTA format.

When you are finished, click OK. If you wish to open the popup again to add additional files, check the Add another box before pressing OK. Each imported structure appears on a separate row of the table. Multi-sequence FASTA files are imported as a batch, with each sequence listed on a separate row.

Here are descriptions of each column in the now-populated table:

  • Job Name displays the name of each query protein sequence or its FASTA title tag. Information in this column can be changed by inserting the cursor and type over the existing text.
  • Residues displays the number of residues in the sequence.
  • Structures displays the path and file name of each structure file.

If you want to delete a job from the table, select the job and press Remove.

Click Submit to submit the job without further customization, or click Next to proceed to the Options screen. If you choose Submit, you can close this dialog as soon as the Close button is enabled.

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