Frequently Asked Questions (FAQ)


  1. What is DEGRONOPEDIA?
  2. What is a degron?
  3. What is needed to run DEGRONOPEDIA?
  4. What inputs can I submit?
  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 for the results?
  10. Can the results be downloaded?
  11. Is there a way to get a better explanation of some calculations performed by the server?
  12. Do I need to create an account to use the server?
  13. Who can see the data I uploaded?
  14. Is it possible to have a copy of the server to run locally?
  15. Can I use the Machine Learning to perform high-throughput predictions of protein N-/C-termini stability?
  16. Can I use DEGRONOPEDIA commercially?
  17. How can I contact the authors?
  18. 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. We recommend to take a video ⚡Quick Tour to see what DEGRONOPEDIA can do for you.

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.

What inputs can I submit?

 There are four allowed input types:
  1. UniProt ID - UniProt ID of a protein from the reference proteome of one of the 11 model organisms: H. sapiens, M. musculus, R. norvegicus, D. rerio, D. melanogaster, C. elegans, S. cerevisiae, S. pombe, A. thaliana, O. sativa, Z. mays
  2. Sequence - sequence in the FASTA format
  3. Structure - a protein monomer structure in the PDB format
  4. Structure + UniProt ID - a protein monomer structure in the PDB format with its corresponding UniProt ID
Read more in the Documentation.

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

 The query protein must contain between 50 and 40.000 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.

How long do I have to wait for the results?

 This depends on several aspects, such as length of the query sequence, server load, length of the queue, and the execution time of your job. Hence, your request may be completed in a few seconds, or in the worst case it may take up to an hour. Requests to analyze multiple sequences can be sent directly to us.

Can the results be downloaded?

 Yes, the results can be downloaded as an xlsx file, with the relevant data saved in separate sheets. The link to download the results is available at the top of each results page.

Is there a way to get a better explanation of some calculations performed by the server?

 All the concepts and implementation details are explained in the Documentation, as well as along the output information within the icons. If you do not find the answer to your question there, please contact us.

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 the user's uploaded data unless there is a specific error or problem. Each job is given an internal random identifier to ensure data privacy. However, in order to monitor the server, we keep statistics on its usage.

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

 No. The server by design is supposed to be an online service. There is no possibility to download the software and run it locally.

Can I use the Machine Learning to perform high-throughput predictions of protein N-/C-termini stability?

 Yes. Users interested in using our Machine Learning models to perform high-throughput predictions of protein N-/C-termini stability can use our standalone software available at github.com/filipsPL/degronopedia-ml-psi.

Can I use DEGRONOPEDIA commercially?

Our proprietary algorithms, including those identifying potential secondary and tertiary degrons, generate data available under the Creative Commons Attribution (CC BY) license. However, it's important to understand that certain limitations apply, particularly concerning commercial usage. This is due to our incorporation of external software and datasets in our processes, which may have their own licensing restrictions. The data presented at this website is made for scientific purposes. Users cannot use commercially data coming from external software and datasets if according to licensing restrictions they are not allowed to do so. Users are advised to review these conditions carefully before applying our data in commercial projects.

Table. List of external datasets/software used by DEGRONOPEDIA along with their licenses.
Name Description License Free to all users?
Degrons List of all degron motifs from different sources Varies; the license for each degron is reported ✅ / ❌
UniProt Proteomes of selected model organisms CC BY 4.0 ✅
AlphaFold Protein Structure Database Structural models for proteomes of selected model organisms CC BY 4.0 ✅
DSSP Software to calculate secondary structure and relative solvent accesibility (RSA) Boost Software License ✅
IUPred3 Software to predict disorder regions based on the query sequence Other ❌
eggNOG5 Dataset of pre-calculated Multiple Sequence Alignments (MSAs)
of orthologs		 CC BY ✅
iPTMNet Dataset of post-translational modifications CC BY-NC-SA ❌
PhosphoSitePlus Dataset of post-translational modifications CC BY-NC-SA ❌
Plant PTM Viewer Dataset of post-translational modifications Not licensed ✅
PLMD Dataset of post-translational modifications Other ✅
BioGRID Dataset of interactome MIT ✅
IntAct Dataset of interactome CC BY ✅
UbiNet 2.0 Dataset of interactome Other ❌
COSMIC Dataset of mutations in human protein-coding genes Other ❌
MEROPS Dataset of experimental proteolytic sites and enzymes GNU Library General Public License ✅
Pyteomics Software for theoretical predictions of proteolysis Apache-2.0 ✅

How can I contact the authors?

 Would you like to share your opinion, suggest a new feature or report a bug? Or maybe you would like to use DEGRONOPEDIA in your research and discuss the possibility of a collaborative project? In any case, please contact Natalia Szulc and Wojciech Pokrzywa.

How can I cite DEGRONOPEDIA?

 Natalia A Szulc, Filip Stefaniak, Małgorzata Piechota, Anna Soszyńska, Gabriela Piórkowska, Andrea Cappannini, Janusz M Bujnicki, Chiara Maniaci & Wojciech Pokrzywa
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons. Nucleic Acids Research, 2024
doi: 10.1093/nar/gkae238