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. Visit fpbase.org for more.

This dataset updated on ,March 1st, 2026, collects FPbase fluorescent protein records (e.g., names, identifiers, sequences, and photophysical properties) for downstream analysis and modeling.

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Quickstart Usage

Install HuggingFace Datasets

Each subset can be loaded into Python using the HuggingFace datasets library. First, install it from the command line:

pip install datasets

Optionally set the cache directory:

export HF_HOME=${HOME}/.cache/huggingface/

Then, from within Python, import the library:

import datasets

Load the Dataset

To load one of the <DATASET ID> subsets, use datasets.load_dataset(...):

dataset_tag = "<DATASET TAG>"
dataset = datasets.load_dataset(
    path="<HF PATH TO DATASET>",
    name=f"{dataset_tag}",
    data_dir=f"{dataset_tag}"
)["train"]

The dataset is loaded as a datasets.arrow_dataset.Dataset:

>>> dataset
<RESULT OF LOADING DATASET MODEL>

This column-oriented format can be accessed directly, converted to a pandas.DataFrame, or exported to parquet:

dataset.data.column("<COLUMN NAME IN DATASET>")
dataset.to_pandas()
dataset.to_parquet("dataset.parquet")

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Dataset Description

Source: 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 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

Excerpts from primary literature can also be entered to store key information that is otherwise difficult to capture within the current database schema.

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Dataset Fields

Raw data is available at fpbase_raw.csv.

Field	Description
name	Protein name
fpbase_id	ID in FPbase
ex_max	Excitation maximum
em_max	Emission maximum
emhex	Emission color (hex)
exhex	Excitation color (hex)
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 type

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Citation

Lambert, TJ (2019) FPbase: a community-editable fluorescent protein database. Nature Methods. doi: 10.1038/s41592-019-0352-8

Licensing

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. Users should attribute the original authors of the corresponding data (referenced on the relevant protein pages).

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Dataset Card Authors

Yijie Luo, Ming Shen, Kaley Chinoy