Frequently Asked Questions


  1. What is DEGRONOPEDIA?
  2. What is a degron?
  3. What is needed to run DEGRONOPEDIA?
  4. What input formats can I use?
  5. What is the minimum and maximum number of amino acids in a query protein?
  6. How many sequences can I upload simultaneously?
  7. Are there any example files?
  8. What is the importance of a degron being a phosphodegron?
  9. How long do I have to wait?
  10. Can the output be downloaded?
  11. Do I need to create an account to use the server?
  12. Who can see the data I uploaded?
  13. Is it possible to have a copy of the server to run locally?
  14. How do I report problems or suggestions?
  15. How can I cite DEGRONOPEDIA?

What is DEGRONOPEDIA?

Degronopedia is a web server that enables you to rapidly explore and visualize integrated data related to protein degrons to understand the functional context of protein turnover better.

What is a degron?

Degron is a short amino acid sequence that serves as a signaling motif directing the proteins possessing them to degradation by the ubiquitin-proteasome system. Read more in the Tutorial.

What is needed to run DEGRONOPEDIA?

DEGRONOPEDIA was tested on major browsers (Chrome, Firefox, Safari). Please let us know if you experience any problems (see About).

What input formats can I use?

There are three allowed input types:
  1. UniProt ID - UniProt ID of a protein from the canonical UniProt proteome of seven model organisms: A. thaliana, S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, or H. sapiens.
  2. Sequence - one sequence at a time in the valid FASTA format.
  3. Structure - a protein monomer structure in the valid PDB format.
Read more in the Tutorial.

What is the minimum and maximum number of amino acids in a query protein?

The query protein must contain between 50 and 8000 canonical-only amino acids.

How many sequences can I upload simultaneously?

Regardless of the input type, it is currently possible to query one protein at a time.

Are there any example files?

Yes, each input type offers possibility to run it on an example. Please try the Load Example option.

What is the importance of a degron being a phosphodegron?

Phospodegron contains one or more phosphorylated residues which may modulate the degron's accessibility. See review.

How long do I have to wait?

This depends on several aspects, such as length of the sequence, server load, and the execution time of your job.
Thus, your request will be completed within seconds, and at worst, it may take up to 2 minutes. Requests for analysis of very long sequences can be sent directly to us (see About).

Can the output be downloaded?

Yes, the output information may be downloaded as an xlsx file, with corresponding data saved to separate sheets.
The appropriate Download Results link is available at the top of the results page.

Do I need to create an account to use the server?

No, DEGRONOPEDIA is free and open to all users and there is no login required.

Who can see the data I uploaded?

There will be no insight into your sequence or structure data unless a specific bug or problem exists. Each job is given an internal random identifier. However, to monitor the server, we keep statistics on server usage.

Is it possible to have a copy of the server to run locally?

No. The server is aimed to be web-based service. As for now, there is no possibility to download the software and run it locally.

How do I report problems or suggestions?

Please contact Natalia Szulc or Wojciech Pokrzywa, and we will try our best to help or fix the problem.

How can I cite DEGRONOPEDIA?

Natalia A. Szulc, Filip Stefaniak, Małgorzata Piechota, Andrea Cappannini, Janusz M. Bujnicki, Wojciech Pokrzywa (2022).
DEGRONOPEDIA - a web server for proteome-wide inspection of degrons
doi: 10.1101/2022.05.19.492622