README.md

---
license: apache-2.0
language:
- en

pretty_name: Morpheus-3D Database

tags:
- protein
- protein-structure
- structural-biology
- bioinformatics
- foldseek
- 3di
- alphafold
- pdb
- metamorphic-proteins
- machine-learning
- dataset

size_categories:
- 1M<n<10M
---

# Morpheus-3D Database

## Overview

The **Morpheus-3D Database** is a comprehensive sequence–structure resource developed to support the **Morpheus-3D** framework for protein fold-switching prediction and structural diversity analysis. It integrates experimentally determined structures from the **Protein Data Bank (PDB)** and high-confidence protein structure predictions from the **AlphaFold Protein Structure Database** into a unified, searchable repository.

Each protein entry contains multiple complementary structural representations, enabling efficient sequence-to-structure mapping, structural alphabet analysis, and rapid retrieval of protein fragments for computational structural biology and machine learning applications.

This repository contains the databases used by the **Morpheus-3D** software and web server.

---

# Dataset Statistics

| Property | Value |
|-----------|-------:|
| Total protein entries | **1,770,688** |
| Total residues | **4,101,250,302** |
| Minimum sequence length | **5 amino acids** |
| Maximum sequence length | **29,668 amino acids** |
| Mean sequence length | **2,316.19 amino acids** |
| Median sequence length | **1,364 amino acids** |

---

# Repository Contents

```
Morpheus3D_sequence_database.zip
Morpheus3D_database_sqlite.zip
README.md
LICENSE
```

---

# File Descriptions

## Morpheus3D_sequence_database.zip

Compressed archive containing the complete Morpheus-3D protein sequence database.

After extraction:

```
Morpheus3D_database.fasta
```

Each protein record contains:

- Protein identifier
- Amino acid sequence
- DSSP secondary structure annotation
- Foldseek 3Di structural alphabet sequence
- Residue-wise AlphaFold pLDDT confidence scores (when available)

### Record Format

```text
>Protein_ID
AMINO_ACID_SEQUENCE
DSSP_SEQUENCE
3DI_SEQUENCE
[pLDDT_VALUES]
```

---

## Morpheus3D_database_sqlite.zip

Compressed archive containing the indexed SQLite database used by the Morpheus-3D prediction pipeline.

After extraction:

```
Morpheus3D_database.sqlite
```

The SQLite database provides:

- Fast protein sequence lookup
- Efficient k-mer indexing
- Rapid structural fragment retrieval
- High-performance database queries
- Direct compatibility with the Morpheus-3D software and web server

---

# Data Sources

The Morpheus-3D Database integrates protein structural information from:

- Protein Data Bank (PDB)
- AlphaFold Protein Structure Database

Protein structures were processed to generate:

- Amino acid sequences
- DSSP secondary structure assignments
- Foldseek 3Di structural alphabet representations
- Residue-wise AlphaFold pLDDT confidence scores (where available)

---

# Applications

The Morpheus-3D Database supports a wide range of computational structural biology and machine learning applications, including:

- Protein fold-switching prediction
- Structural diversity analysis
- Protein language model development
- Foldseek 3Di structural alphabet research
- Sequence–structure relationship studies
- Protein engineering
- Computational structural biology
- Machine learning on protein structural representations

---

# Download

This repository contains two downloadable archives:

| Archive | Description |
|----------|-------------|
| **Morpheus3D_sequence_database.zip** | FASTA-based protein sequence database containing amino acid sequences, DSSP annotations, Foldseek 3Di structural alphabet sequences, and residue-wise AlphaFold pLDDT confidence scores. |
| **Morpheus3D_database_sqlite.zip** | Indexed SQLite database for high-performance sequence lookup, k-mer indexing, and rapid integration with the Morpheus-3D software and web server. |

Download and extract the archive(s) required for your application before using them with the Morpheus-3D software.

---

# Citation

If you use the Morpheus-3D Database or its derived structural representations in your research, please cite:

Sreeharsh Kuniyil, Vijay Subramanian, Akanksha Arun, Anand Lakshmanan, Ashok Sekhar, Anand Srivastava. **Morpheus-3D: Structural Diversity-Guided Detection and Localization of Protein Fold Switching.** bioRxiv (2026). https://doi.org/10.64898/2026.08.16.745091

# Contact

For questions, bug reports, or feature requests, please open an issue in this repository or contact the corresponding authors of the Morpheus-3D project.

---

# Acknowledgements

The Morpheus-3D Database was developed as part of the Morpheus-3D framework for large-scale prediction and localization of protein fold-switching behavior using sequence-derived structural diversity. It is intended to facilitate reproducible research in structural bioinformatics, protein science, and machine learning.