Lim Heo

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" biorxiv.org/content/10.110…

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: nobelprize.org/prizes/chemist…

Our team at Bristol Myers Squibb in Cambridge, MA is looking for a student for a Spring 2025 co-op. …stolmyerssquibb.wd5.myworkdayjobs.com/BMS/job/Cambri…

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: arxiv.org/abs/2409.17808 Github: github.com/bjing2016/mdgen

Contrats Martin! 🎉🎉

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: evolutionaryscale.ai/blog/esm3-rele…

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 linkedin.com/jobs/view/3954…

for the folks who missed @sokrypton's excellent presentation and discussion of #AlphaFold3 last week, you can now check out the recording 👇 youtu.be/qjFgthkKxcA

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: arxiv.org/abs/2405.20313 1/8 🧵

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

@chiw00k 누군가가 그 연못과 바위를 찾으러 갔다는데, 찾을 수 없었다고합니다. npr.org/2020/03/13/815…

수페리어호에서 가장 큰 섬인 로예일섬에 호수가 있는데 거기 섬이 하나 있고 그 섬에 연못이 있는데 거기 바위가 하나 있다네요. 그래서 그 바위는 세상에서 가장 큰 호수의 가장 큰 섬의 가장 큰 호수의 가장 큰 섬의 가장 큰 호수의 가장 큰 섬이 됩니다.

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

Something weird is going on with some parts of the Stanford network and @biorxivpreprint access. Can't access anything from my laptop by access from my phone 4G. Anyone else having this problem?

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. go.nature.com/3ZLIcw1

“SaProt: Protein Language Modeling with Structure-aware Vocabulary” An ESM1b-sized PLM pre-trained on structural data that outperforms other PLMs on various tasks biorxiv.org/content/10.110… github.com/westlake-repl/…

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 🗓️➡️ recruitment.irbbarcelona.org/jobs/2447575-i…

@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.

저걸 K-푸드라고 이름 붙이기는 좀 아닌 거 같아요. 제가 듣기로는 미국 한인들이 수십개씩 사가느라 순식간에 매진된 거랍니다. 저도 사러 갔는데 완판되었다고 10월에나 다시 들어 오니 그때 오라고 하더라고요. ㅋ imnews.imbc.com/replay/2023/nw…

@sucheol_shin @PRX_Life Congratulations on your new work!

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]

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! huggingface.co/docs/transform…

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

Way too many preprints today. Yall need to stop being so productive

Statistical Mechanics: Theory and Molecular Simulation, 2nd Edition, now available on Amazon [amazon.com/Statistical-Me…] and will be available on Oxford University Press later this month for the electronic version, October for the hardcover version.