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Short answer
FPbase is a free, community-editable online database of fluorescent proteins. It holds sequences, accession IDs, lineages, fluorescence attributes, structural data and literature references for each protein, plus tools for viewing spectra and configuring a microscope. It is cited as Lambert 2019, Nature Methods 16, 277-278.
Definition and scope
According to its own About page (read 2026-11-07), FPbase is a free and open-source, community-editable database created in 2018 by Talley Lambert at Harvard Medical School. Each protein page gathers the amino acid sequence, accession IDs, lineages and mutations, fluorescence attributes, structural data and references, and users can add excerpts from the primary literature. The site footer carries a CC BY-SA 4.0 badge.
For background on the proteins themselves, see the CASRAI guides on GFP structure, size and spectra and mCherry spectra and properties, which use FPbase-style values. For obtaining plasmids encoding a protein you found, see the Addgene repository guide.
Types or related concepts: which FPbase tool answers which question
| Question | FPbase feature | What its own pages say |
|---|---|---|
| Do these fluorophores overlap with my filters and light source? | Spectra viewer | Compare spectra with common filters and light sources |
| What will my own microscope’s configuration actually excite and collect? | Microscopes | Build a spectra viewer customized for the specifications of your microscope |
| How did this protein derive from its ancestors? | Lineage explorer | Lists lineages and mutations on protein pages |
| Which known protein does my sequence resemble? | FP BLAST | Sequence search tool listed on the About page |
| Is a FRET pair workable? | FRET calculator | Listed on the About page |
| Can I pull values into my own analysis? | REST API and GraphQL | JSON by default, CSV via format=csv; GraphQL covers proteins, dyes, spectra, filters, cameras, light sources, microscopes and references |
| How do I share a panel of proteins? | Protein collections | Public collections have static IDs and URLs |
Where it matters for labs, clinics or supply decisions: spectra viewer and microscope configurations
The spectra viewer overlays excitation and emission spectra against common filters and light sources. The Microscopes feature lets you define your own instrument, so the overlay reflects your filter sets and sources rather than a generic example. A saved microscope configuration has a static ID and URL, which makes it possible to point readers of a methods section at the exact configuration used.
Using the API
The API page (read 2026-11-07) documents /api/proteins/, /api/proteins/<slug>/, /api/proteins/basic/ and /api/proteins/spectra/ (limit up to 200), with Swagger docs at /api/docs/ and a GraphQL endpoint at /graphql/. Pagination uses page and page_size (default 100), and fields= and include_fields= trim the response. Unrecognized parameters return a 400. Exposed attributes include excitation and emission maxima, quantum yield, extinction coefficient, lifetime, maturation, brightness, pKa and bleach rate (default state only). The API page states no rate limits and no API-specific license, so neither should be assumed.
How to cite FPbase: a reproducibility checklist
The Cite page (read 2026-11-07) gives the following. A practical checklist follows from it:
- Cite the database: Lambert TJ (2019) FPbase: a community-editable fluorescent protein database. Nature Methods 16, 277-278, DOI 10.1038/s41592-019-0352-8.
- If you relied on the software, cite the source code at github.com/tlambert03/FPbase.
- For each individual fluorescent protein, cite its original paper; FPbase lists these in the reference sections of the protein page.
- Link the static URL of any public protein collection or custom microscope configuration you used.
Common misunderstandings
- FPbase is not the original source of a protein’s measurements. It is a curated aggregation; the Cite page directs you to the original papers for individual proteins.
- Entries are community-edited. Check the referenced primary literature before relying on a value, because fluorescence attributes depend on the conditions of the original measurement.
- The API is not a stated open-data licence. The site footer’s CC BY-SA 4.0 badge is a site-level statement; the API page does not state its own terms.
FAQ
What does FPbase stand for?
It is the Fluorescent Protein Database, a community-editable resource described in Lambert 2019.
Who created FPbase?
Talley Lambert of Harvard Medical School, in 2018, per the About page.
Can I download data from FPbase?
The API returns JSON by default and CSV with format=csv; GraphQL is also available.
How do I cite a specific protein found on FPbase?
Cite the protein’s original paper, listed in its references section, in addition to the FPbase paper.
Sources
- FPbase, About: fpbase.org/about/ (read 2026-11-07)
- FPbase, Cite: fpbase.org/cite/ (read 2026-11-07)
- FPbase, API: fpbase.org/api/ (read 2026-11-07)
- Lambert TJ (2019) Nature Methods 16, 277-278. doi:10.1038/s41592-019-0352-8
