Simon Kozlov
@sim0nsays.bsky.social
Researcher at MIT, generative AI for protein design
Reposted by Simon Kozlov
Great to have our manuscript with @sokrypton.org 's lab describing AfCyDesign finally out in @natcomms.bsky.social . Structure prediction, sequence redesign, de novo hallucination of cyclic peptides, and some binder design examples in this version.
rdcu.be/em0vA
rdcu.be/em0vA
Cyclic peptide structure prediction and design using AlphaFold2
Nature Communications - AfCycDesign: Cyclic offset to the relative positional encoding in AlphaFold2 enables accurate structure prediction, sequence redesign, and de novo hallucination of cyclic...
rdcu.be
May 23, 2025 at 7:07 PM
Great to have our manuscript with @sokrypton.org 's lab describing AfCyDesign finally out in @natcomms.bsky.social . Structure prediction, sequence redesign, de novo hallucination of cyclic peptides, and some binder design examples in this version.
rdcu.be/em0vA
rdcu.be/em0vA
Reposted by Simon Kozlov
Oh wow great @haleaziz.bsky.social piece on a 2018 case in which Trump’s ICE screwed up and erroneously deported a guy. AND THEY BROUGHT HIM BACK because why wouldn’t they?
We’re in a much darker place now.
Free link:
www.nytimes.com/2025/04/15/u...
We’re in a much darker place now.
Free link:
www.nytimes.com/2025/04/15/u...
April 16, 2025 at 12:59 AM
Oh wow great @haleaziz.bsky.social piece on a 2018 case in which Trump’s ICE screwed up and erroneously deported a guy. AND THEY BROUGHT HIM BACK because why wouldn’t they?
We’re in a much darker place now.
Free link:
www.nytimes.com/2025/04/15/u...
We’re in a much darker place now.
Free link:
www.nytimes.com/2025/04/15/u...
Reposted by Simon Kozlov
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
April 8, 2025 at 12:17 PM
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
Reposted by Simon Kozlov
BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse)
To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜
Paper: www.cell.com/developmenta...
To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜
Paper: www.cell.com/developmenta...
December 4, 2024 at 10:12 PM
BOOSTER, a newly identified orphan gene, supercharges photosynthesis and, when overexpressed, boosts height of poplars by up to 200% (at least in greenhouse)
To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜
Paper: www.cell.com/developmenta...
To make it even more interesting, part of the gene seems derived from a poplar fungus-farming ant 🐜
Paper: www.cell.com/developmenta...
Biology is amazing
Delighted to publish my new molecular animation:
DNA Break Repair by Homologous Recombination
youtu.be/Xe-83tBcxhs
DNA Break Repair by Homologous Recombination
youtu.be/Xe-83tBcxhs
DNA Break Repair by Homologous Recombination (2024) Drew Berry wehi.tv
YouTube video by WEHImovies
youtu.be
December 5, 2024 at 3:21 AM
Biology is amazing
Reposted by Simon Kozlov
💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)
November 30, 2024 at 5:14 AM
💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)
Fully accepting nothing may work out is a surprisingly effective way to work something out.
Here’s the catch: knowing this fights against acceptance.
Here’s the catch: knowing this fights against acceptance.
November 29, 2024 at 1:02 PM
Fully accepting nothing may work out is a surprisingly effective way to work something out.
Here’s the catch: knowing this fights against acceptance.
Here’s the catch: knowing this fights against acceptance.
I would love for a social network to exist where questions like this get a meaningful discussion. I don’t think Twitter had it even if it’s best days, with a few exceptions when tweet randomly goes viral.
Can we make it work here? That would take the whole community to a next level.
Can we make it work here? That would take the whole community to a next level.
November 25, 2024 at 2:49 AM
I would love for a social network to exist where questions like this get a meaningful discussion. I don’t think Twitter had it even if it’s best days, with a few exceptions when tweet randomly goes viral.
Can we make it work here? That would take the whole community to a next level.
Can we make it work here? That would take the whole community to a next level.
Reposted by Simon Kozlov
November 20, 2024 at 1:27 PM
Noticed that whenever I see a tweet I like, the first thing I do is check if author is on BlueSky. Glad to be here!
November 20, 2024 at 3:42 PM
Noticed that whenever I see a tweet I like, the first thing I do is check if author is on BlueSky. Glad to be here!