.
@compchemm
Computational Structural Biologist |
PyMoLFold - Just Added support for: github.com/ullahsamee/PyM… - Uniprot sequence import - Models: Chai-1, Boltz-1 now works both for protein and protein-ligands - SMILES/CCDCodes works Download latest zip and try it. Thanks to Colby T. Ford for initiating this exciting project.
🧬✨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…
Toward De Novo Protein Design from Natural Language: Propose Pinal, a 2-stage generative framework, avoiding end-to-end text-protein generation. Design an optimal sampler to integrate both stages. Outperform ESM3 when prompting with text. #ProteinDesign biorxiv.org/content/10.110…
Bush Babies and Fennec Fox loves the de novo designed binders youtube.com/watch?v=mDytS9…
A complete list of Molecular Dynamics Research groups worldwide - perfect for anyone looking for any positions nature.com/articles/s4159…
#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! 🤩
A total of 7 de novo binders in the competition, 6 made with BindCraft!
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.
PROTEIN DESIGN COMPETITION ROUND 2 The long awaited results are here -- and they don’t disappoint! 📈 We doubled the number of proteins we tested in our lab from 200 to 400! 🧬 Out of those 400 proteins, 378 expressed (95% expression rate!) 🚀 Out of those 378 expressed…
Connection with Google Scholar @PhDVoice #phdlife #academia
Is there something you wish Gemini could do with other apps or services? Tell us what extensions you’re looking for in the comments.
CASp16 Pharmaceutical protein-Ligand Challenge ullahsamee.github.io/resultscasp/ credit: Mike Gilson UCSD #CASP16
AF3 has clearly not solved the antibody-antigen prediction problem seeing the #CASP16 results…
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…
We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months.
"As strongly requested by the reviewers, here we cite some references"😂 @PhDVoice @PostdocVoice #AcademicTwitter sciencedirect.com/science/articl…
