---
license: mit
language:
- en
---
# FPbase: The Fluorescent Protein Database
More than 1000 experimental fluorescent proteins with structured and searchable fluorescence polarization (FP) data
https://www.fpbase.org.

## Quickstart Usage

### installation
Clone repo and cd into directory

    $git clone https://github.com/tlambert03/FPbase.git
    $cd FPbase
    
Create and activate environment using python 3.13 with conda

    $conda create -n FPbase python=3.13
    $conda activate FPbase
    
(optional) Install uv

    $curl -LsSf https://astral.sh/uv/install.sh | sh
    
Install python requirements for local development

    $uv sync
    $sudo apt install postgresql postgresql-contrib -y
    $curl -fsSL https://deb.nodesource.com/setup_20.x | sudo -E bash -
    $sudo apt install -y nodejs
    $npm i -g pnpm
    
Install frontend requirements

    $pnpm install
    
Create database, and apply migrations

    $createdb fpbase
    $python backend/manage.py migrate
    
Start and test dev servers 

    $pnpm dev
    
### 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.