---
license: mit
language: en
---
# FPbase: The Fluorescent Protein Database
FPbase is a free, open-source, community-editable database of fluorescent proteins and their properties, aimed at aggregating structured, searchable information useful to the imaging community and FP developers. https://www.fpbase.org.
This dataset packages FPbase fluorescent protein records (e.g., names, identifiers, sequences, and photophysical properties) as machine-readable files suitable for downstream analysis and modeling.

## Quickstart Usage

### Install HuggingFace Datasets package
Each subset can be loaded into python using the HuggingFace [datasets](https://huggingface.co/docs/datasets/index) library. First, from the command line install the `datasets` library

  $ pip install datasets

Optionally set the cache directory, e.g.

  $ HF\_HOME=${HOME}/.cache/huggingface/
  $ export HF\_HOME

then, from within python load the datasets library

  \>\>\> import datasets

### fetch database information 
Run the [pull_fpbase.py](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/blob/main/src/pull_fpbase.py)

    $python /src/pull_fpbase.py

## Output description
Check the [fpbase_raw.csv](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/tree/main/data)
- **name: protein name**
- **fpbase_id: ID in FPbase**
- **ex_max: excitation maximum**
- **em_max: emission maximum**
- **emhex: emission color**
- **exhex: emission color**
- **ext_coeff: extinction coefficient**
- **qy: quantum yield**
- **lifetime_ns: lifetime(ns)**
- **pdb: PDB ID**:
- **genbank: genbank ID**
- **uniprot: Uniprot ID**
- **aggregation: oligomeric state**
- **switch_type: photo-switching types**
  
### Dataset Description
(https://github.com/tlambert03/FPbase)
FPbase is a free and open-source, community-editable database for fluorescent proteins (FPs) and their properties. 
The primary objective is to aggregate structured and searchable FP data that is of interest to the imaging community and FP developers. 
Each protein in the database has a dedicated page showing amino acid sequence, accession IDs (e.g. GenBank, UniProt), evolution lineages and mutations, fluorescence attributes, structural data, references that introduced or characterized the protein, 
and more. Excerpts from primary literature can be entered to store key information about a protein that is otherwise difficult to capture within the current database schema.

## Liscensing
FPbase states that data in the FPbase archive are “free of all copyright restrictions” and made fully and freely available for both non-commercial and commercial use, and that users should attribute the original authors of the corresponding data (referenced on the relevant protein pages).

## Dataset Card Authors
Yijie Luo, Ming Shen