Update README.md

README.md

@@ -26,11 +26,11 @@ size_categories:
 
 ## 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 predictions from the **AlphaFold Protein Structure Database** into a unified, searchable repository.
+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 database used by the **Morpheus-3D** software and web server.
+This repository contains the databases used by the **Morpheus-3D** software and web server.
 
 ---
 
@@ -50,7 +50,7 @@ This repository contains the database used by the **Morpheus-3D** software and w
 # Repository Contents
 
 ```
-Morpheus3D_database_fasta.zip
+Morpheus3D_sequence_database.zip
 Morpheus3D_database_sqlite.zip
 README.md
 LICENSE
@@ -60,9 +60,9 @@ LICENSE
 
 # File Descriptions
 
-## Morpheus3D_database_fasta.zip
+## Morpheus3D_sequence_database.zip
 
-Compressed archive containing the complete Morpheus-3D protein database.
+Compressed archive containing the complete Morpheus-3D protein sequence database.
 
 After extraction:
 
@@ -72,11 +72,11 @@ Morpheus3D_database.fasta
 
 Each protein record contains:
 
-1. Protein identifier
-2. Amino acid sequence
-3. DSSP secondary structure annotation
-4. Foldseek 3Di structural alphabet sequence
-5. Residue-wise AlphaFold pLDDT confidence scores (when available)
+- Protein identifier
+- Amino acid sequence
+- DSSP secondary structure annotation
+- Foldseek 3Di structural alphabet sequence
+- Residue-wise AlphaFold pLDDT confidence scores (when available)
 
 ### Record Format
 
@@ -114,8 +114,8 @@ The SQLite database provides:
 
 The Morpheus-3D Database integrates protein structural information from:
 
-- **Protein Data Bank (PDB)**
-- **AlphaFold Protein Structure Database**
+- Protein Data Bank (PDB)
+- AlphaFold Protein Structure Database
 
 Protein structures were processed to generate:
 
@@ -128,7 +128,7 @@ Protein structures were processed to generate:
 
 # Applications
 
-The Morpheus-3D Database can be used for:
+The Morpheus-3D Database supports a wide range of computational structural biology and machine learning applications, including:
 
 - Protein fold-switching prediction
 - Structural diversity analysis
@@ -143,16 +143,29 @@ The Morpheus-3D Database can be used for:
 
 # Download
 
-The database is distributed as compressed ZIP archives to reduce download size and facilitate efficient storage. Extract both archives before using them with the Morpheus-3D software.
+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 regarding the Morpheus-3D database or software, please open an issue in this repository or contact the corresponding authors of the Morpheus-3D project.
+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. The database is intended to support reproducible research in structural bioinformatics, protein science, and machine learning.
+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.