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Deniz Akpinaroglu

@dakpinaroglu.bsky.social

799 followers 121 following 6 posts

UCBerkeley and UCSF Bioengineering PhD candidate @KortemmeLab | NSF GRFP Fellow | Cat Mom

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

Code for our preprint is open-sourced! 🚀 Explore Frame2seq on GitHub: github.com/dakpinaroglu... 📓 Try Frame2seq out in our Colab notebook: colab.research.google.com/github/dakpi... 💻 Also try it out with: `pip install frame2seq`

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

🧵 Work with Kosuke Seki, Amy Guo, Eleanor Zhu, Mark Kelly, and Tanja Kortemme

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

🧵 Our "Top0" design (0% seq. id. to Top7) is soluble, monomeric, folded, and the HSQC spectrum reveals that "Top0" likely maintains a fold identical to Top7!

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

🧵 We design and test novel proteins for de novo backbones. Most significantly, we evaluate a 0% sequence identity design for the famous Top7 fold

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

🧵 Frame2seq is an IPA-based encoder-only model that achieves state-of-the-art native sequence recovery

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Deniz Akpinaroglu @dakpinaroglu.bsky.social · 27/12/2023

🧵 Super excited to share our model Frame2seq and our preprint “Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space” www.biorxiv.org/content/10.1...

biorxiv.org

Structure-conditioned masked language models for protein sequence design generalize beyond the nativ...

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

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