RNAMotifDB

RNAMotifDB is a research workflow for RNA 3D motif extraction, structural clustering, representative template selection, and template-guided RNA 3D structure prediction.

Main Findings

• Constructed a reusable RNA motif template database from experimentally determined RNA structures.
• Implemented motif extraction, clustering, representative-template selection, and template-search workflows.
• Enabled rapid identification of structurally related motifs for downstream RNA 3D modeling.
• Generated representative motif libraries suitable for template-guided assembly and structure prediction.

Installation Notes :

VFold is required for the full VFold-based pipeline and should be installed from the official site : - https://rna.physics.missouri.edu/vfold_software_download/vfoldpipeline_download.html

Additional external tools may be required depending on the workflow step:

VFoldPipeline VFold2D VFold3DLA DSSR/3DNA C++ compiler Python dependencies can be installed with:

pip install -r requirements.txt


## Repository Structure

- `src/database_building/`  
  Core scripts for building the RNA motif template database from motif PDB structures.

- `src/template_search_pipeline/`  
  Scripts and modified VFold components for RNA 2D input processing, motif extraction, template search, template trimming, and marker generation.

- `src/analysis_reports/`  
  Supporting scripts for database summaries, RNA-type annotation, clustering reports, and visualization.

- `docs/`  
  Workflow documentation and example commands.

- `data_examples/`  
  Small example input files.

- `results/`  
  Small example outputs from the workflow.

- `templates/`  
  Example VFold-style template database outputs.

- `figures/`  
  Workflow diagrams and result visualizations.

## Main Workflow

RNA motif PDB structures  
↓  
Sequence grouping  
↓  
RMSD-based structural clustering  
↓  
Representative template selection  
↓  
VFold-style database generation  
↓  
RNA 2D motif extraction  
↓  
Template search  
↓  
Template-guided RNA 3D modeling support  

## Notes

This repository documents a research workflow. Some components depend on the original VFoldPipeline/VFold3DLA environment, compiled binaries, and expected directory structure. Standalone scripts and example files are provided where possible.