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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
>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 in your research, please cite the accompanying Morpheus-3D publication (citation to be added upon publication).
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.
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