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I'm excited to share that I'll be joining @MITBiology as an Asst Prof. in Jan 2024! Come join us! 🤓🧪🖥️🧬
Sergey Ovchinnikov
3,903 posts
Sergey Ovchinnikov
@sokrypton
Scientist, Assistant Professor @MITBiology, #FirstGen, ProteinBERTologist, 🇺🇦
No Human is illegal.
Moving to: bsky.app/profile/sokryp…
- For my latest attempt at introducing proteins to students, I made a Google Colab Notebook that predicts proteins from a single sequence. I asked the students to tweak the sequence to get a helix or two helices or... (1/5) colab.research.google.com/github/sokrypt…
- Really cool sculpture of Top7 by @mtyka . Celebrating 10 years of IPD @UWproteindesign (check out the reflection in the glass) 🤯
00:00 - RoseTTAFold updated to be All-Atom... biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications ... and diffusion🤯biorxiv.org/content/10.110…
- Excited to see colabfold published! nature.com/articles/s4159… Special thanks to @thesteinegger and @milot_mirdita (for MMseqs2) without whom I would have never considered to preprint let alone attempt to publish our notebook! (1/3)
- End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman biorxiv.org/content/10.110… A fun collaboration with Samantha Petti, Nicholas Bhattacharya, @proteinrosh, @JustasDauparas, @countablyfinite, @keitokiddo, @srush_nlp & @pkoo562 (1/8)
00:00 - AlphaFold inverted to hallucinate denovo proteins of up to 600 amino acids in length🤯 (animation below shows the designed protein docked into CryoEM density) Exciting work with: @chrisfrank662, @AKhoshouei, Yosta de Stigter, Dominik Schiewitz, @ShihaoFeng18, @hendrik_dietz
00:00 - Lots of interesting work recently on using #RoseTTAFold and/or #AlphaFold to predict protein-protein interactions: biorxiv.org/content/10.110… biorxiv.org/content/10.110… onlinelibrary.wiley.com/doi/full/10.10… biorxiv.org/content/10.110… biorxiv.org/content/10.110…
- Ever wondered how many amino acids you can mutate to alanine and AlphaFold2 still predicts same structure? 🤔For denovo design Top7 (1QYS), single-sequence mode, it's 60%. (1/2)
- AlphaFold3 reproduced and params/code released. 🤩Technical Report of HelixFold3 for Biomolecular Structure Prediction The PaddleHelix research team at Baidu have released their AlphaFold3 replication under an open-source noncommercial license. Performance approaches that of AlphaFold3. abs: arxiv.org/abs/2408.16975 website:
- Successfully predicted one of the @foldit denovo designs using #alphafold in google-colab😎 (1 model, no template, single sequence input, and no amber refine, ~2 mins). Notebook if anybody wanna try input your favorite sequence: colab.research.google.com/drive/1qWO6Arw…
- Ok. I'm sold. 🤓 Prompt "implement dynamic programming in NumPy to align two sequences"
- We've been working on adding AlphaFold v2.3.1 support to ColabFold. 😎 Here is the notebook for those interested in testing: colab.research.google.com/github/sokrypt… (1/5)
- DALL·E 3 prompt "protein structure, surrounded by small molecules resembling amino acid sidechains"🧑🎨🖼️ (1/10)
