What is this?

Using this web app, you can run NetAvg calculations. NetAvg takes an ensemble of protein conformations as input and returns, as output, a single conformation that best represents the ensemble. For further details, see our Proteins article, Extracting representative structures from protein conformational ensembles. To download the source code for NetAvg, visit our GitHub repository.

To submit jobs to NetAvg through this web interface, you'll need an ensemble of conformations for your protein of interest. The accepted input formats are: (1) a .pdb containing multiple frames; (2) a .zip file comprised of .pdb files. The input is limited to 1000 conformations or less. Inputs larger than 1000 conformations will return an error. Here is a sample input trajectory that you can try:

How to use the NetAvg app

  1. Click the Persona button to login. You can login with any valid email address.
  2. After logging in, you'll see the NetAvg Home page. The left side is a list of your NetAvg jobs. If this is your first time logging in, the list will be empty. The right side is the job submission form, from which you can launch new NetAvg calculations.
  3. To submit a job, first specify a title for your job. Then, click the Choose File button in the "Trajectory" field. In the dialog that appears, select the .pdb or .zip file for your conformational ensemble from your computer.
  4. As an optional step, you can modify the number of neighbors that will be used to generate the representative structure from your conformational ensemble.
  5. Click the Submit button. Your job will appear in the job list on the left side of the interface with a status of "submitted".
  6. Clicking Refresh Job List will refresh the status of your jobs. When your job is complete, the status will change from "submitted" to "done" (calculation time will vary based on protein length, size of conformational ensemble, and number of jobs in queue). At that point, you can click on the name of your job and view the results.
  7. On the results page shows click on Download Output PDB to save the representative conformation from your submitted ensemble. You can also click the Delete button to remove the job from your list if you no longer need the results. Note: deleted jobs are not recoverable so delete with care.