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Update README branding and add example usage demo #41

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14ebe5f
chore: corrected logo file path locations and include example usage demo
harryswift01 Sep 7, 2026
51c65ae
chore: reorder paragraph placement within `README.md`
harryswift01 Sep 7, 2026
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14 changes: 7 additions & 7 deletions README.md
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<p align="center" width="100%">
<img src="https://raw.githubusercontent.com/CCPBioSim/branding/refs/heads/main/logos/prepmd/prepmd-logo-black-text.svg" width="256px" >
</div>

prepmd
==============================

| Category | Badges |
|----------------|--------|
Expand All @@ -13,13 +11,15 @@

A utility to automatically prepare structures from the PDB for molecular dynamics simulation and perform minimisations and simple MD simulations.

## Example usage
<p align="center">
<img src="docs/_static/logos/prepmd-logo-white-text.svg#gh-dark-mode-only" alt="prepmd logo" width="300"/>
<img src="docs/_static/logos/prepmd-logo-black-text.svg#gh-light-mode-only" alt="prepmd logo" width="300"/>
<img src="docs/source/_static/logos/prepmd-logo-white-text.svg#gh-dark-mode-only" alt="prepmd logo" width="300"/>
<img src="docs/source/_static/logos/prepmd-logo-black-text.svg#gh-light-mode-only" alt="prepmd logo" width="300"/>
</p>


## Example usage
<img width="768" height="432" alt="demo" src="https://github.com/user-attachments/assets/f7785a4d-ef54-428d-b193-1cb6413bc21e" />

## Features
* Automatically download structures, sequences and metadata from the PDB, PDB-REDO, EMDB and UNIPROT
* Automatically fill missing loops with MODELLER or pdbfixer
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