DocumentationFoldify
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).
We are pleased to announce that AlphaFold3 is now accessible for use. To access the software, you must first read the Alphafold3 model terms of use. Next, request access to the appropriate group and confirm that you have read and accepted the terms.
Dashboard
After successful login you will be redirected to the Dashboard View that consists of two main sections: New Job and Last Computed Jobs.
New Job Section
This section consists of the cards with available Tools - AlphaFold, ColabFold, OmegaFold and ESMFold.
By pressing the Run Job button you can start a new computation with the selected tool. You will be redirected to the form page where you can fill in the parameters for the computation.
Last Computed Jobs Section
This section consists of a table listing the last computed jobs. You can find your protein name and click the View Result button to display the result in the browser. You can also download the results by clicking the Download button.
Computed jobs table is separated into two parts - My Jobs and Public Jobs. Public part contains all public results, while My Jobs section contains only your computations.
Running Jobs Section
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 (Make results public checkbox).
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.
Molstar Viewer
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
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.
Result Tabs
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.
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