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Title: GitHub - coder-chicken/RFdiffusion: Code for running RFdiffusion · GitHub

Open Graph Title: GitHub - coder-chicken/RFdiffusion: Code for running RFdiffusion

X Title: GitHub - coder-chicken/RFdiffusion: Code for running RFdiffusion

Description: Code for running RFdiffusion. Contribute to coder-chicken/RFdiffusion development by creating an account on GitHub.

Open Graph Description: Code for running RFdiffusion. Contribute to coder-chicken/RFdiffusion development by creating an account on GitHub.

X Description: Code for running RFdiffusion. Contribute to coder-chicken/RFdiffusion development by creating an account on GitHub.

Opengraph URL: https://github.com/coder-chicken/RFdiffusion

X: @github

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Domain: github.com

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LICENSE	https://github.com/coder-chicken/RFdiffusion/blob/main/LICENSE
LICENSE	https://github.com/coder-chicken/RFdiffusion/blob/main/LICENSE
README.md	https://github.com/coder-chicken/RFdiffusion/blob/main/README.md
README.md	https://github.com/coder-chicken/RFdiffusion/blob/main/README.md
setup.py	https://github.com/coder-chicken/RFdiffusion/blob/main/setup.py
setup.py	https://github.com/coder-chicken/RFdiffusion/blob/main/setup.py
README	https://github.com/coder-chicken/RFdiffusion
License	https://github.com/coder-chicken/RFdiffusion
	https://github.com/coder-chicken/RFdiffusion#rfdiffusion
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/diffusion_protein_gradient_2.jpg
	https://github.com/coder-chicken/RFdiffusion#description
the RFdiffusion paper	https://www.biorxiv.org/content/10.1101/2022.12.09.519842v1
	https://github.com/coder-chicken/RFdiffusion#table-of-contents
RFdiffusion	https://github.com/coder-chicken/RFdiffusion#rfdiffusion
Description	https://github.com/coder-chicken/RFdiffusion#description
Table of contents	https://github.com/coder-chicken/RFdiffusion#table-of-contents
Getting started / installation	https://github.com/coder-chicken/RFdiffusion#getting-started--installation
Conda Install SE3-Transformer	https://github.com/coder-chicken/RFdiffusion#conda-install-se3-transformer
Get PPI Scaffold Examples	https://github.com/coder-chicken/RFdiffusion#get-ppi-scaffold-examples
Usage	https://github.com/coder-chicken/RFdiffusion#usage
Running the diffusion script	https://github.com/coder-chicken/RFdiffusion#running-the-diffusion-script
Basic execution - an unconditional monomer	https://github.com/coder-chicken/RFdiffusion#basic-execution---an-unconditional-monomer
Motif Scaffolding	https://github.com/coder-chicken/RFdiffusion#motif-scaffolding
The "active site" model holds very small motifs in place	https://github.com/coder-chicken/RFdiffusion#the-active-site-model-holds-very-small-motifs-in-place
The inpaint_seq flag	https://github.com/coder-chicken/RFdiffusion#the-inpaint_seq-flag
A note on diffuser.T	https://github.com/coder-chicken/RFdiffusion#a-note-on-diffusert
Partial diffusion	https://github.com/coder-chicken/RFdiffusion#partial-diffusion
Binder Design	https://github.com/coder-chicken/RFdiffusion#binder-design
Practical Considerations for Binder Design	https://github.com/coder-chicken/RFdiffusion#practical-considerations-for-binder-design
Fold Conditioning	https://github.com/coder-chicken/RFdiffusion#fold-conditioning
Generation of Symmetric Oligomers	https://github.com/coder-chicken/RFdiffusion#generation-of-symmetric-oligomers
Using Auxiliary Potentials	https://github.com/coder-chicken/RFdiffusion#using-auxiliary-potentials
Symmetric Motif Scaffolding.	https://github.com/coder-chicken/RFdiffusion#symmetric-motif-scaffolding
A Note on Model Weights	https://github.com/coder-chicken/RFdiffusion#a-note-on-model-weights
Things you might want to play with at inference time	https://github.com/coder-chicken/RFdiffusion#things-you-might-want-to-play-with-at-inference-time
Understanding the output files	https://github.com/coder-chicken/RFdiffusion#understanding-the-output-files
Docker	https://github.com/coder-chicken/RFdiffusion#docker
Conclusion	https://github.com/coder-chicken/RFdiffusion#conclusion
	https://github.com/coder-chicken/RFdiffusion#getting-started--installation
Google Colab Notebook	https://colab.research.google.com/github/sokrypton/ColabDesign/blob/v1.1.1/rf/examples/diffusion.ipynb
	https://github.com/coder-chicken/RFdiffusion#conda-install-se3-transformer
Anaconda or Miniconda	https://conda.io/projects/conda/en/latest/user-guide/install/index.html
NVIDIA's implementation of SE(3)-Transformers	https://developer.nvidia.com/blog/accelerating-se3-transformers-training-using-an-nvidia-open-source-model-implementation/
	https://github.com/coder-chicken/RFdiffusion#get-ppi-scaffold-examples
	https://github.com/coder-chicken/RFdiffusion#usage
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/main.png
	https://github.com/coder-chicken/RFdiffusion#running-the-diffusion-script
Hydra configs	https://hydra.cc/docs/configure_hydra/intro/
	https://github.com/coder-chicken/RFdiffusion#basic-execution---an-unconditional-monomer
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/cropped_uncond.png
	https://github.com/coder-chicken/RFdiffusion#motif-scaffolding
Constrained Hallucination and RFjoint Inpainting	https://www.science.org/doi/10.1126/science.abn2100#:~:text=The%20binding%20and%20catalytic%20functions%20of%20proteins%20are,the%20fold%20or%20secondary%20structure%20of%20the%20scaffold.
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/motif.png
	https://github.com/coder-chicken/RFdiffusion#the-active-site-model-holds-very-small-motifs-in-place
	https://github.com/coder-chicken/RFdiffusion#the-inpaint_seq-flag
	https://github.com/coder-chicken/RFdiffusion#a-note-on-diffusert
	https://github.com/coder-chicken/RFdiffusion#partial-diffusion
Vazquez-Torres et al., BioRxiv 2022	https://www.biorxiv.org/content/10.1101/2022.12.10.519862v4.abstract
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/partial.png
	https://github.com/coder-chicken/RFdiffusion#binder-design
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/binder.png
	https://github.com/coder-chicken/RFdiffusion#practical-considerations-for-binder-design
	https://github.com/coder-chicken/RFdiffusion#selecting-a-target-site
	https://github.com/coder-chicken/RFdiffusion#truncating-your-target-protein
	https://github.com/coder-chicken/RFdiffusion#picking-hotspots
	https://github.com/coder-chicken/RFdiffusion#binder-design-scale
	https://github.com/coder-chicken/RFdiffusion#sequence-design-for-binders
this GitHub repo	https://github.com/nrbennet/dl_binder_design
	https://github.com/coder-chicken/RFdiffusion#binder-design-filtering
here	https://github.com/nrbennet/dl_binder_design
	https://github.com/coder-chicken/RFdiffusion#fold-conditioning
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/fold_cond.png
	https://github.com/coder-chicken/RFdiffusion#generation-of-symmetric-oligomers
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/olig2.png
	https://github.com/coder-chicken/RFdiffusion#using-auxiliary-potentials
	https://github.com/coder-chicken/RFdiffusion#symmetric-motif-scaffolding
	https://github.com/coder-chicken/RFdiffusion/blob/main/img/sym_motif.png
	https://github.com/coder-chicken/RFdiffusion#a-note-on-model-weights
	https://github.com/coder-chicken/RFdiffusion#things-you-might-want-to-play-with-at-inference-time
	https://github.com/coder-chicken/RFdiffusion#understanding-the-output-files
	https://github.com/coder-chicken/RFdiffusion#docker
official Docker docs	https://docs.docker.com/get-docker/
Finch	https://github.com/runfinch/finch
	https://github.com/coder-chicken/RFdiffusion#conclusion
Readme	https://github.com/coder-chicken/RFdiffusion#readme-ov-file
View license	https://github.com/coder-chicken/RFdiffusion#License-1-ov-file
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