sk @compchemm
Computational Structural Biologist | Joined April 2017-
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Germinal setup RTX5090 CUDA 13 github.com/ullahsamee/ger…
A complete list of Molecular Dynamics Research groups worldwide - perfect for anyone looking for any positions nature.com/articles/s4159…
AlphaFold3 at - CASP16 biorxiv.org/content/10.110…
#ScientificBreakthrough: AI-designed protein targets heart failure mechanism. First demonstration of a new, lab-verified protein designed to target cellular energy depletion in heart failure. Experimental validation confirms successful synthesis, improved stability, and…
🔥 Benchmark Alert! MotifBench sets a new standard for evaluating protein design methods for motif scaffolding. Why does this matter? Reproducibility & consistent evaluation have been lacking—until now. Paper: arxiv.org/abs/2502.12479 | Repo: github.com/blt2114/MotifB… A thread ⬇️
Full-atom MPNN (FAMPNN) - a sequence design method that explicitly models both sequence identity and sidechain conformation. biorxiv.org/content/10.110… code: github.com/richardshuai/f…
CyclicBoltz1, fast and accurately predicting structures of cyclic peptides and complexes containing non-canonical amino acids using ... biorxiv.org/content/10.110… #biorxiv_bioinfo
Bindcraft is killing it! 🤩
Here are the 10 binders from me and Lennart that got selected for testing, all expressed, top left was 5th best ranked binder. We only went for beta sheeted proteins we designed for round 1, no additional optimisation.
Here are the 10 binders from me and Lennart that got selected for testing, all expressed, top left was 5th best ranked binder. We only went for beta sheeted proteins we designed for round 1, no additional optimisation. https://t.co/4jJ5bHC1hp
AF3 has clearly not solved the antibody-antigen prediction problem seeing the #CASP16 results…
🧬✨Excited to share our online demo " Natural language → De Novo Protein design" Live demo: http://113.45.254.183:8888/ The demo version Pinal is 1.2B.🔬 You try very detailed textual prompt up to 500 words. biorxiv.org/content/10.110…
🧬✨Excited to share our online demo " Natural language → De Novo Protein design" Live demo: http://113.45.254.183:8888/ The demo version Pinal is 1.2B.🔬 You try very detailed textual prompt up to 500 words. biorxiv.org/content/10.110… https://t.co/XNQP0siuPd
Our experience with #alphafold3 🤖 (code recently released) and some of our most recent #cryoEM 🔬 structures (thread below) nature.com/articles/s4158… nature.com/articles/s4146…
After showing that AF2 can be used to design very large proteins by performing #RSO, I am happy to share another fun project we did: the #af2cycler @sokrypton @hendrik_dietz biorxiv.org/content/10.110…
The #AlphaFold 3 model code and weights are now available for academic use. We @GoogleDeepMind are excited to see how the research community continues to use AlphaFold to address open questions in biology and new lines of research. github.com/google-deepmin…
The #AlphaFold 3 model code and weights are now available for academic use. We @GoogleDeepMind are excited to see how the research community continues to use AlphaFold to address open questions in biology and new lines of research. github.com/google-deepmin…
"As strongly requested by the reviewers, here we cite some references"😂 @PhDVoice @PostdocVoice #AcademicTwitter sciencedirect.com/science/articl…
Finally, out in @ScienceMagazine today, our work on de novo protein design. Together with @HattoriLab , @sokrypton & @hendrik_dietz we showed how we can drastically improve AF2 based hallucination, surpassing, or reaching SOTA diffusion models doi.org/10.1126/scienc…
Is it time for the protein emoji to return? Can we overcome the past unicode rejection now with the tailwinds of the Nobel Prize? Can proteins be recognized as important as 🫘 or 🙎or 🥀?
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:…
1/ 🧬 Excited to share CHEAP, our new work on compressed protein embeddings. We characterize the joint distribution of p(sequence, structure) in ESMFold's latent space, and find cool tidbits on compressibility, tokenizability, and pathologies: biorxiv.org/content/10.110… 🧵
EMDB - EMPIAR @EBI @EMDB_EMPIAR
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