This topic is a general overview on how to set up, run and view a NovaFold Antibody prediction through the Protean 3D interface. If you are instead running NovaFold Antibody locally on a Linux or Macintosh machine, see Run Nova applications locally. If you are running NovaFold Antibody online, see Run Nova applications through the DNASTAR website.

  1. If you are not currently logged into NovaCloud Services, open the NovaCloud Services view and log in. If you are already logged in, you can skip ahead and launch the NovaFold Antibody wizard by doing any of the following:

    • From the Welcome screen, click Structure Prediction on the left and then New antibody structure with NovaFold Antibody on the right.

    • Choose Modeling > Antibody Structure Prediction > New NovaFold Antibody Prediction.

    • From the NovaCloud Services view, press the NovaFold Antibody button.

    • From the Predictions view, use the small black triangle in the top-left corner to choose NovaFold Antibody.
  1. Follow the steps in the three NovaFold Antibody wizard screens: Sequences, Options and Submit.
  1. Use View > NovaCloud Services > Predictions to monitor run status and open or download predictions from within the Predictions view. NovaFold Antibody results can be opened on any computer running Protean 3D 12.1 and higher; a NovaFold license is not required to view results.

Open results appear as a new project tab in Protean 3D. Unlike NovaFold and NovaDock, NovaFold Antibody has no specialized Report view. Instead, all Protean 3D views and panels are enabled, as for any structure file. However, the NovaFold Antibody project differs from a typical Protean 3D in two ways:

  • In the Molecules section, the light and heavy chains are designated as L and H.

  • In the Style section, a new item called NovaFold Antibody Loop is available By using the corresponding expand triangles, you can expand this item and its subtopics to reveal the three light (L1, L2, L3) and/or three heavy (H1, H2, H3) chain annotations.

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