README.md

---
license: mit
---

# DMS-Fold2 Benchmark Dataset

This repository contains the benchmark datasets used to evaluate **DMS-Fold2**. The files are organized into two benchmark sets:

- **CASP/CAMEO targets** (`casp_cameo_targets/`)
- **Mega-scale targets** (`megascale_targets/`)

Each target includes the sequence and experimental data required to reproduce the benchmark inputs.

## Directory Structure

```text
paper_benchmarks/
├── casp_cameo_targets/
│   ├── alignments.tar.gz
│   ├── fastas/
│   ├── pdbs/
│   ├── dm_csvs/
│   └── sm_csvs/
└── megascale_targets/
    ├── alignments.tar.gz
    ├── fastas/
    ├── pdbs/
    ├── dm_csvs/
    └── sm_csvs/
```

## Contents

### `alignments.tar.gz`

Compressed archive containing one directory per protein target with precomputed multiple sequence alignments (MSAs).

### `fastas/`

FASTA sequences for each benchmark protein.

### `pdbs/`

PDB files for each benchmark protein.

### `dm_csvs/`

Double-mutant deep mutational scanning (DMS) datasets used as input to DMS-Fold2.

### `sm_csvs/`

Single-mutant deep mutational scanning (DMS) datasets used as input to DMS-Fold2.

## Benchmark Sets

### `megascale_targets`

Benchmark proteins selected from the Mega-scale DMS collection.

### `casp_cameo_targets`

Benchmark proteins from CASP14, CASP15, and CAMEO.

## Citation

If you use this dataset, please cite the accompanying DMS-Fold2 publication.

``` TBD
```
[![Static Badge](https://img.shields.io/badge/DMS--Fold2-GitHub-blue)](https://github.com/LindertLab/DMS-Fold2)
[![Static Badge](https://img.shields.io/badge/DMS--Fold2-Weights-green)](https://huggingface.co/LindertLab/DMS-Fold2)
[![Static Badge](https://img.shields.io/badge/DMS--Fold2-Training--Dataset-yellow)](https://huggingface.co/datasets/LindertLab/DMS-Fold2-Training-Dataset)