| --- |
| 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. |
