Lim Heo

Started a new position at Bristol-Myers Squibb!

[Lim Heo @huhlim]

CG models can be quickly (~s) and very accurately (<0.5 A, ~2 MolProbity score) reconstructed to atomistic structures using ML.
"One particle per residue is sufficient to describe all-atom protein structures" https://t.co/0v2Fke5Q9P

[The Nobel Prize @NobelPrize]

Some words of wisdom from this year's chemistry laureate David Baker, whose work has made it possible to design new proteins from scratch.

Read more and join us on tomorrow 8 December to hear his Nobel Prize lecture: https://t.co/10fEOSEDEr

[Lim Heo @huhlim]

Our team at Bristol Myers Squibb in Cambridge, MA is looking for a student for a Spring 2025 co-op.
https://t.co/a9tGhLBwAO

[Leo Zang @LeoTZ03]

Generative Modeling of Molecular Dynamics Trajectories | NeurIPS 24' |📸"molecular video"
- MDGEN, a flow-based model for MD trajectories, with various capabilities (forward simulation, interpolation, upsampling, and molecular design)
- Tokenize structure as Roto-Translation and Torsion Angles. Define known frames as key frames and represent other atoms in the trajectory as offsets
- Build based on Scalable Interpolant Transformer (SiT) and use Dirichlet flow matching to model amino acid identities
- Replace attention with Hyena and show proof-of-concept in Inpainting Design and 100k-frame trajectories
Link: https://t.co/Br1RKBcq1E
Github: https://t.co/B3ouoeq5GC

[Lim Heo @huhlim]

Contrats Martin! 🎉🎉

[Alex Rives @alexrives]

We have trained ESM3 and we're excited to introduce EvolutionaryScale.

ESM3 is a generative language model for programming biology. In experiments, we found ESM3 can simulate 500M years of evolution to generate new fluorescent proteins.

Read more: https://t.co/iAC3lkj0iV

[Lim Heo @huhlim]

Our team at BMS is seeking an expert in #NGS data analysis and #machinelearning for antibody therapeutics. If you're interested in this opportunity, don't miss out! #hiring
https://t.co/qmXe8rWttL

[Boston Protein Design and Modeling Club @ProteinBoston]

for the folks who missed @sokrypton's excellent presentation and discussion of #AlphaFold3 last week, you can now check out the recording 👇
https://t.co/12DhAJFUlR

[Guillaume Huguet @Guillaume_hu]

Introducing FoldFlow-2, a new SOTA sequence-conditioned protein generative model!

work w/ @DreamFoldAI James V @FatrasKilian Eric TL @PabloLemosP @riashatislam @ChengHaoLiu1 @jarridrb @tara_aksa @mmbronstein @AlexanderTong7 @bose_joey

Arxiv: https://t.co/p5sypnhXct
1/8 🧵

[Jason Yim @json_yim]

Sharing an early preprint of my Microsoft AI4Science summer internship project. We developed SE(3) flow matching for protein backbone generation. Compared to SE(3) diffusion, we find our method achieves higher designability, faster sampling, with a way simpler implementation. 1/8

[Lim Heo @huhlim]

@chiw00k 누군가가 그 연못과 바위를 찾으러 갔다는데, 찾을 수 없었다고합니다.
https://t.co/aHoNZzpyU5

[Lim Heo @huhlim]

@anshulkundaje @biorxivpreprint Phew... I am not the only blocked one.
For me, Chrome is blocked, Safari works.

[nature @Nature]

South Korean scientists’ outcry over planned R&D budget cuts.

In a nation with historically high levels of spending on research and development, the proposed cuts have provoked a strong response. https://t.co/K2ZDb0wTu6

[Diego del Alamo @DdelAlamo]

“SaProt: Protein Language Modeling with Structure-aware Vocabulary”

An ESM1b-sized PLM pre-trained on structural data that outperforms other PLMs on various tasks

https://t.co/XmUb36qHsH
https://t.co/IUADYNQKnb

[MDDB @mddbEU]

We are looking for a Project Manager 🧑‍💼👩‍💼to help us with the MDDB project implementation. Do you have knowledge about databases, data management, MD simulations and project management skills🔖? Would you like to join the team? Last days to apply 🗓️➡️
https://t.co/bXUkEwGLTS

[Lim Heo @huhlim]

@chiw00k 저도 이거 사러 트죠에 가긴했는데 매진이더라구요. 근데 비한국인 직원에게 있냐고 물어보며 스몰톡 했을때 자기도 먹어봤는데 맛있었고 떨어져서 아쉽다그러고, 계산하시는 분에게도 얘기했더니 자기도 못먹어서 아쉽다그러더라구요.

[Lim Heo @huhlim]

@sucheol_shin @PRX_Life Congratulations on your new work!

[Sucheol Shin @sucheol_shin]

Very excited that one of my major postdoc works has been just published online @PRX_Life ! The title of the paper is: From Effective Interactions Extracted Using Hi-C Data to Chromosome Structures in Conventional and Inverted Nuclei. More details in the following thread! [1/n]

[Matthew Carrigan @carrigmat]

The ESM models (including ESMFold!) have all been ported to @huggingface and will remain there even though the ESM team has been disbanded. We have example notebooks (look under 'Biological Sequences') if you've never tried it before! https://t.co/Y2zFrtXIVw

[Lim Heo @huhlim]

@DdelAlamo So many preprints everyday and hard to follow up. Thank you for tweeting many precious works with your comments!

[Tuckerman Group @GroupTuckerman]

Statistical Mechanics: Theory and Molecular Simulation, 2nd Edition, now available on Amazon [https://t.co/hTQT0vPf9b] and will be available on Oxford University Press later this month for the electronic version, October for the hardcover version.