DOI: 10.5281/zenodo.17713589
title: ProFam: Open-Source Protein Family Language Modeling for Fitness Prediction and Design - The ProFam Atlas Dataset
title: ProFam Atlas: a collection of diverse protein families for training protein family language models

description: ProFam-Atlas Dataset

The ProFam-Atlas is a curated, large-scale dataset of protein sequences grouped by varying definitions of "protein family". It was developed to train the ProFam-1 protein family language model (pfLM) and supports research in protein design, fitness prediction, and evolutionary biology. Full details of dataset creation can be found in:

ProFam: Open-Source Protein Family Language Modeling for Fitness Prediction and Design (Wells et al., 2025.)


 

Dataset Composition

The dataset aggregates protein family definitions from multiple sources, ranging from structure-centric clusters to deep multiple sequence alignments (MSAs) and functional groupings.

 

### 1. FoldSeek AlphaFold Database Clusters

- **Source:** FoldSeek AlphaFold Database (AFDB) clusters.

- **Definition:** Structure-centric families formed by first clustering sequences (50% identity, 90% coverage) and then clustering structures (FoldSeek E-value ≤ 0.01).

- **Statistics:** Approximately **2.3 million families** comprising **30 million sequences**.

 

 

### 2. OpenProteinSet MSAs (Re-clustered)

- **Source:** OpenFold OpenProteinSet (subset of 270k maximally diverse MSAs).

- **Definition:** Re-processed to ensure length consistency and cleaner alignments. Aligned sequences were split at contiguous gaps (>10 residues), filtered for length (≥90 residues), and re-clustered using MMseqs2 (30% sequence identity, 70% coverage).

- **Statistics:** **37 million families** comprising **246 million sequences**.

 

### 3. TED FunFams

- **Source:** The Encyclopedia of Domains (TED) and CATH Functional Families (FunFams).

- **Definition:** Continuous domains from TED mapped to CATH FunFam HMM profiles. Matches were redundancy-reduced (50% identity) and further clustered (30% identity, 80% overlap) to ensure sequence and length consistency.

- **Statistics:** **38,000 families** comprising **765,000 sequences**.

 

### 4. UniRef90 Single Sequences

- **Source:** UniRef90 (release 2025_01).

- **Definition:** Single sequences included to cover regions of the protein universe not captured by the family-based groupings.

- **Statistics:** **205 million single sequences**.

 

File Structure and Format

The dataset is distributed as a collection of paired `.mapping` and `.sequences` files. This structure allows for efficient random access to specific families without loading entire files into memory.

 

Mapping Files (`*.mapping`)

Contains the index information for each family.

- **Format:**

- Line 1: Family Identifier (prefixed with `>`).

- Line 2: The name of the corresponding `.sequences` file, followed by a colon `:`, and a comma-separated list of byte offsets (or entry indices) for the sequences belonging to that family.

 

**Example:**

```text

>1.25.40.900_ted.fasta.0

train_001.sequences:0,2,4,5,6,7,8...

```

 

Sequence Files (`*.sequences`)

Contains the actual protein sequences in a FASTA-like format.

- **Format:**

- Header line starting with `>` containing the sequence identifier (and potentially metadata).

- Sequence line containing the amino acid sequence.

 

**Example:**

```text

>AF-A0A1H4DYA3-F1-model_v4_TED03/0.0

EWAKAETAANAVINSGIYTLNKDLNLRLAEQYLIRAEARAQLGNLAGAVADVDSIRSKAGLPQLDNSITQPALLLAIEKERKAELFGEWGHRWFDLKRTPAVAGGGKTRAD

>AF-A0A1W1ZJU1-F1-model_v4_TED01/1.1

LLMQAEAENEVNGPTQVAYNAVNEVRHRAGLPDLTPGLAKEAFFNALVDERAHELCFEGFRKWDLIRWNMLGAKIRATQTALKAYRANFPYVAGDNF

```

 

Citation

If you use the ProFam-Atlas dataset in your research, please cite the following preprint:

ProFam: Open-Source Protein Family Language Modeling for Fitness Prediction and Design

Wells et al., 2025.