Help & Support
Find guides, documentation, and support for using CD-CODE.
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Getting Started
Learn the basics of the CD-CODE interface, how to search, and how to interpret charts and data.
- Use the search bar on the Home page to find proteins, condensates, c-mods or diseases.
- Browse data categories using the large icons/buttons on the Home page.
- Charts and statistics are available in the Statistics page.
- See the About page for a full overview of CD-CODE features.
Video Guides
Watch our video guides to learn how to use CD-CODE and its curation tools.
How to add a new condensate?
API & Documentation
Access our REST API documentation and learn how to fetch live data from CD-CODE.
Go to API DocsContact / Support
Need help or you have any questions? Reach out to us or check our FAQ below.
FAQ
How can I find a condensate?
On the home page you can search for a condensate by entering the condensate name (e.g. Stress Granule); this will take you to the Search Results page where matching condensates (biomolecular, infectious and/or synthetic) are listed. You can filter down the results further by species.
How can I find a protein?
On the home page you can search for a protein by name, UniProt ID, or gene; this will take you to the Search Results page where matching proteins are listed in annotated species.
How are CD-CODE entries referenced in UniProt?
You can find the cross-references in UniProt under the “Subcellular localization” section. All currently cross-referenced protein entries can be located at https://www.uniprot.org/uniprotkb?query=(database:CD-CODE).
How can I search for proteins and condensates?
Search: Input the specific term to find the related protein, condensate, c-mod, condensatopathy, or species.
Filter: You can input part of the term to filter tables and narrow results.
Can I search for a specific species?
Yes. Input the species name or taxon ID (e.g. Homo sapiens, Danio rerio) in the Search field, or use the filter function on the Condensates and Proteins pages.
Where/how do I find the experimental evidence for a protein-condensate pair?
Experimental evidence annotations are stored in a condensate-centric way. Evidence with associated PubMed IDs is recorded in columns corresponding to specific evidence types identified in publications related to particular condensate–protein pairs.
What are confidence scores?
Confidence score for a protein belonging to a condensate (max. 5 stars):
1 star (⭐): PubMed reference annotated;
2 stars (⭐⭐): High-throughput experiment (e.g., mass spectrometry);
3 stars (⭐⭐⭐): Annotated with in vitro experimental evidence;
4 stars (⭐⭐⭐⭐): Annotated with in cellulo experimental evidence;
5 stars (⭐⭐⭐⭐⭐): Annotated with in vivo experimental evidence.
Confidence score for a condensate (max. 5 stars) is the median of the confidence scores of its member proteins. Please refer to the About page for more details.
Can I access CD-CODE programmatically?
Yes. See the CD-CODE REST API documentation. To request an API token, contact mail@cd-code.org. You do not need to sign up to use the REST API.
Do I need to sign up to use CD-CODE?
No, you don’t need to sign up to use the database web interface or download our data dumps.
Why do I need to sign up?
You only need to sign up if you want to become a contributor or maintainer of CD-CODE (for example, to use the curation tool). See the curation tool documentation for details.
Cannot find your question among the FAQs?
Please send an email to mail@cd-code.org if you cannot find the answer to your question here.