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https://github.com/lamm-mit/proteinmechanicsdiffusiondesign

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Host: GitHub
URL: https://github.com/lamm-mit/proteinmechanicsdiffusiondesign
Owner: lamm-mit
License: mit
Created: 2023-09-29T17:34:57.000Z (about 1 year ago)
Default Branch: main
Last Pushed: 2024-02-10T11:52:17.000Z (9 months ago)
Last Synced: 2024-02-10T12:37:19.342Z (9 months ago)
Language: Jupyter Notebook
Size: 4.45 MB
Stars: 2
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

# ProteinMechanicsDiffusionDesign

## End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a protein language diffusion model

B. Ni, D.L. Kaplan, M.J. Buehler, ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model. Sci. Adv. 10, eadl4000 (2024). DOI: 10.1126/sciadv.adl4000

![plot](./documents/Figure1.png)

### Summary
Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. Here we report a generative model that predicts protein designs to meet complex nonlinear mechanical property-design objectives. Our model leverages deep knowledge on protein sequences from a pre-trained protein language model and maps mechanical unfolding responses to create novel proteins. Via full-atom molecular simulations for direct validation, we demonstrate that the designed proteins are novel, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, as well as the detailed unfolding force-separation curves. Our model offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, using mechanical features as target to enable the discovery of protein materials with superior mechanical properties.

### Installation and use

A [colab notebook](./notebook_for_colab/pLDM_inference_standalone_colab.ipynb) is included in this repository that feature the trained model.

To install and run, just click the "open in Colab" badge and choose to run all.
Note that, the first run may take time as it includes downloading and installing packages and the trained model.
The pretrained model is hosted at [this huggingface repository](https://huggingface.co/lamm-mit/ProteinMechanicsDiffusionDesign).

### Reference