Foldify

Foldify is a web application based on Alphafold tools available at https://foldify.cloud.e-infra.cz, after login via e-INFRA CZ AAI (a valid MetaCenter account is required).

Dashboard

After successful login you will be redirected to the Dashboard View. Firstly, you can see the cards with available Tools - AlphaFold, ColabFold, OmegaFold and ESMFold. Each card contains button Run Job that redirects you to the form for chosen tool. Below the Tool Cards you can see the list of previous computations that is separated into two tables - My Jobs and Public Jobs. In the My Jobs section you can see all your computations, in the Public Jobs section you can see all public computations.

If you are currently running a computation, you can see it in the Running Jobs table in the Dashboard View. This table only appears when there is an active computation, otherwise it is hidden. Your active computation can be Queued, Running or Succeeded.

Running a Computation

After choosing a tool, you will be redirected to the form page where you can fill in the parameters for the computation.

The only required parameters are the Protein Sequence and the Job Name, everything else can be left default. You can change the name of the job, but it must be unique (you cannot run multiple computations with the same name), otherwise you will be prompted to enter a different name or check the Force Computation checkbox.

By default, all calculation results are public, i.e. everyone who is able to log in can see them, but the name of the user who initiated the calculation is not shown. If this is not desired, publication can be disabled.

After filling in the parameters, you can start the calculation by clicking the Run Job button. When compuatation finishes, you will receive an email notification.

Viewing Results

If you want to preview the computed results, you can do so from the Last Computed Jobs table on the dashboard. You can find your protein name and click the View Result button to display the result in the browser. The viewer is interactive and allows rotation and panning. You can also download the results by clicking the Download button. Please note, that the results are in most cases large files and can take some time to download. After closing the dialog window downloading process will be cancelled.

In the Results page you can also find the Mol* viewer, which is a more complex viewer for the results. You can open it by clicking the Mol* logo below the embedded 3D viewer.

Plddt score is also displayed in the Results page, which is a measure of the model confidence. The higher the score, the more confident the model is. Data is displayed for each model as graph.

Further you can explore Configuration tab, where you can see the parameters of the computation. And Technical Output tab, where you can see the logs of the computation.