Reposted by Kyle TretinaAlbert Vilella, PhD. @albertvilella.bsky.social · 09/11/2025@allthingsapx.bsky.social on the new Biohub initiative by the Zucks 442
Reposted by Kyle TretinaMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 21/09/2025MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.comnature.comGPU-accelerated homology search with MMseqs2 - Nature MethodsGraphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio... 417463
Kyle Tretina @allthingsapx.bsky.social · 16/09/2025Near-real-time protein structures change science: It means: → Next-gen protein AI data waves → Interactive protein design loops (DMTA in hours) → Proteome-scale insights with fewer resources It means the bottleneck doesn't have to be compute. It's close (preprint below). 150
Kyle Tretina @allthingsapx.bsky.social · 30/08/2025Does anyone here care about biomolecular AI? Who should I follow? 010
Kyle Tretina @allthingsapx.bsky.social · 15/07/2025🧬 Introducing La‑Proteina: a partially‑latent flow‑matching model that co‑generates sequence + all‑atom structure for proteins up to 800 aa 🧬 Side‑chains live in latents, backbone explicit → 75 % codesign & SOTA motif scaffolds 🔥 110
Kyle Tretina @allthingsapx.bsky.social · 15/07/2025I'm at ICML 2025! DM me if you want to chat. @icmlconf.bsky.social #ICML2025 #icml25 #BioNeMo 000
Kyle Tretina @allthingsapx.bsky.social · 13/06/2025Boltz-2 just dropped: open-source AI that predicts both protein complex folds ✚ binding affinities in one shot 🚀 This is a win for protein AI, but let's not forget MSAs, the bioinformatics backbone many structure models lean on. 172
Kyle Tretina @allthingsapx.bsky.social · 13/06/2025MMseqs2-GPU is available as a downloadable NVIDIA NIM microservice (MSA-Search)! 100
Reposted by Kyle TretinaKarsten Kreis @karstenkreis.bsky.social · 04/03/2025📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models" #ICLR2025 (Oral Presentation) 🔥 Project page: research.nvidia.com/labs/genair/... 📜 Paper: arxiv.org/abs/2503.00710 🛠️ Code and weights: github.com/NVIDIA-Digit... 🧵Details in thread... (1/n) 13910
Reposted by Kyle TretinaKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 07/12/2024"Are there at least 3 simulations per simulation condition with statistical analysis?" From @commsbio.bsky.social's "Reliability and reproducibility checklist for molecular dynamics simulations" (doi.org/10.1038/s420...) IMO the number 3 is meaningless and could equally well be 1 or 1000 2195
Reposted by Kyle TretinaFrank Noe @franknoe.bsky.social · 06/12/2024Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1... 21441147
Kyle Tretina @allthingsapx.bsky.social · 06/12/2024DiffDock was the first time a traditional drug discovery simulation task was represented as a generative AI task AFAIK. Recent DiffDock versions + other DL models are advancing rapidly + solving real problems for researchers. Let's have a balanced conversation about it. arxiv.org/abs/2412.02889arxiv.orgDeep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking WorkflowsThe diffusion learning method, DiffDock, for docking small-molecule ligands into protein binding sites was recently introduced. Results included comparisons to more conventional docking approaches, wi... 120
Reposted by Kyle TretinaMartin Pacesa @martinpacesa.bsky.social · 30/11/2024#CASP16 results are in! Template-based VFold seems to be lead method for nucleic acid structure prediction! AlphaFold2 and 3 still seem to be best methods for protein monomer and complex prediction. 28623
Kyle Tretina @allthingsapx.bsky.social · 19/11/2024If you're building AI models for drug discovery, you should check out the newly open-source #BioNeMo Framework: code: github.com/NVIDIA/bione... paper: arxiv.org/abs/2411.10548 docs: docs.nvidia.com/bionemo-fram... explainer: t.co/7MOamSChGNgithub.comGitHub - NVIDIA/bionemo-framework: BioNeMo Framework: For building and adapting AI models in drug discovery at scaleBioNeMo Framework: For building and adapting AI models in drug discovery at scale - NVIDIA/bionemo-framework 094
Kyle Tretina @allthingsapx.bsky.social · 16/11/2024Friends, Real-time, accurate protein structure prediction has never felt so imminent. Code: github.com/soedinglab/m... Publication: www.biorxiv.org/content/10.1... Blog: developer.nvidia.com/blog/boost-a... Press: blogs.nvidia.com/blog/japan-s... 030
Reposted by Kyle TretinaAnshul Kundaje @anshulkundaje.bsky.social · 14/11/2024developer.nvidia.com/blog/boost-a... Boost Alphafold2 Protein Structure Prediction with GPU-Accelerated MMseqs2 Nice improvements in speeddeveloper.nvidia.comBoost Alphafold2 Protein Structure Prediction with GPU-Accelerated MMseqs2 | NVIDIA Technical BlogThe ability to compare the sequences of multiple related proteins is a foundational task for many life science researchers. This is often done in the form of a multiple sequence alignment (MSA)… 35315
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Now available – DiffDock 2.0 NIM This latest #NVIDIANIM update offers computational chemists and researchers a significant boost with 16% improved accuracy in identifying potential protein-small molecule interactions with Test for free: build.nvidia.com/mit/diffdock...build.nvidia.comdiffdock model by mit | NVIDIA NIMPredicts the 3D structure of how a molecule interacts with a protein. 000
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Now available – an updated RFdiffusion NIM This #NVIDIANIM enables researchers to efficiently design protein therapeutic candidates 1.9x faster due to accelerations in the inference engine, making their preclinical research smarter and less expensive. Test for free: build.nvidia.com/ipd/rfdiffus...build.nvidia.comrfdiffusion model by ipd | NVIDIA NIMA generative model of protein backbones for protein binder design. 000
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Accelerated computing is powering a new era in protein structure prediction, now with speed-of-light multiple sequence alignments. #MMseqs2GPU now makes #AlphaFold2 predictions faster and more efficient than ever. 1/🧵 developer.nvidia.com/blog/boost-a...developer.nvidia.comBoost Alphafold2 Protein Structure Prediction with GPU-Accelerated MMseqs2 | NVIDIA Technical BlogThe ability to compare the sequences of multiple related proteins is a foundational task for many life science researchers. This is often done in the form of a multiple sequence alignment (MSA)… 100
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Accelerated computing is revolutionizing protein structure prediction, starting with lightning-fast multiple sequence alignments. Read more about #AlphaFold and #MMseqs2GPU: developer.nvidia.com/blog/boost-a...developer.nvidia.comBoost Alphafold2 Protein Structure Prediction with GPU-Accelerated MMseqs2 | NVIDIA Technical BlogThe ability to compare the sequences of multiple related proteins is a foundational task for many life science researchers. This is often done in the form of a multiple sequence alignment (MSA)… 010
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Have you seen the innovation coming out of Japan recently? 👀 blogs.nvidia.com/blog/japan-s...blogs.nvidia.comJapan Develops Next-Generation Drug Design, Healthcare Robotics and Digital Health PlatformsJapan is pursuing sovereign AI initiatives supporting nearly every aspect of healthcare. They're highlighted at the NVIDIA AI Summit Japan. 000
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024Analyzing extensive scientific literature and real-world evidence, Muse delivers comprehensive research and identifies optimal patient profiles and recruitment strategies, including materials tailored for diverse populations. formation.bio/blog/introdu...formation.bioIntroducing MuseFormation Bio collaborates with Sanofi and OpenAI to Introduce Muse, a first of its kind AI tool to accelerate patient recruitment in drug development. 010
Kyle Tretina @allthingsapx.bsky.social · 13/11/2024I can't help but think TDC-2 is a peek into the future of therapeutic AI, where multimodal data integration and single-cell precision drive discovery. biorxiv.org/content/10.1...biorxiv.org 010