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 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 3, AlphaFold 2, 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.

AlphaFold 2, ColabFold, OmegaFold and ESMFold

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.

AlphaFold 3

AlphaFold 3 is the latest version of the AlphaFold protein structure prediction model. Foldify offers three different modes of submission for AlphaFold 3: Basic Submission, Advanced Submission, and JSON Submission.

• Basic Submission: This mode is designed for users who want to quickly submit a protein sequence for structure prediction without delving into advanced options. It provides a simplified interface with essential parameters.
• Advanced Submission: This mode is intended for users who want to customize their submission with advanced options. It allows for more control over the prediction process, including the ability to specify custom ligands, atom bonds and upload CCD file.
• JSON Submission: This mode is for users who want to submit a JSON file containing the protein sequence and other parameters. It is useful for batch submissions or for users who prefer to work with JSON files.

By default, all calculation results are private, i.e. only you can see them. If you want to share your results with collegues, you can do so by checking Make results public checkbox. In this case, the result is shown in Public Jobs Table and you can share the computation with link.

After filling in the parameters, you can start the computation by clicking the Run Job button. When the computation 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. Find the protein name and click the View Result button to display the result in the browser. Visualization is provided by Mol* Viewer, which is a web-based molecular visualization tool. It allows you to view the protein structure in 3D and interact with it. 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.

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.

FAQ

Why did my computation failed?

One way to find out how your computation failed is to view the logs and find an error warning there. To view the logs, go to the Results page and click on the Technical Output tab. Here you can see the logs of the computation. If you find an error message, you can try to fix it and run the computation again. If you are not sure what the error message means, you can contact us for help via k8s@ics.muni.cz.