Very excited to share our new preprint where we develop MIC, a deep metric learning tool for classifying waters & ions in experimental structures; fantastic collaboration with the extremely talented Laura Shub and Selina Liu from the Keiser lab! biorxiv.org/content/10.110…

Boltz v0.4.0 is here! Today, we’re releasing our full data processing pipeline, making it easier than ever to build on top of Boltz. This release also includes our evaluation code and new results. Oh, and also pocket conditioning :)

Validation of a Coarse-Grained Martini 3 Model for Molecular Oxygen | Journal of Chemical Theory and Computation pubs.acs.org/doi/10.1021/ac…

i’m hiring! come work with our amazing neuralplexer development team to help increase the conformational accuracy of our protein structure predictions! jobs.ashbyhq.com/iambic-therape…

Analyzing Atomic Interactions in Molecules as Learned by Neural Networks #machinelearning #compchem pubs.acs.org/doi/abs/10.102…

🚀 Check out our latest review, "Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery", now published in Molecular Pharmaceutics (ACS Publications )! 🧪📖 🔗 Read here: doi.org/10.1021/acs.mo…

Molecular dynamics study of stiffness and rupture of axonal membranes sciencedirect.com/science/articl…

Martini 3 - IDP is out! Improved parameters for disordered proteins, great work from Liguo Wang: nature.com/articles/s4146…

MartiniGlass: a Tool for Enabling Visualization of Coarse-Grained Martini Topologies | Journal of Chemical Information and Modeling pubs.acs.org/doi/10.1021/ac…

CGsmiles: A Versatile Line Notation for Molecular Representations across Multiple Resolutions | Journal of Chemical Information and Modeling pubs.acs.org/doi/10.1021/ac…

We have brought GROMACS, PyMOL, and ChimeraX together through MCP!🤖 🧪 🔬 Molecule MCP: github.com/ChatMol/molecu… GROMACS Agent: github.com/ChatMol/gromac… Streamline your workflows with LLMs! #AIScience #ComputationalChemistry #ClaudeAI

Quantum chemistry is intrinsically beautiful. Addition of cyanide in acidic condition onto formaldehyde (SMD solvation model in water). #chemistry #reaction #quantum

New preprint: TS2CG v2, building and simulating membranes with any shape and lateral organisation. We got Martini Globe, Martini Möbius strip and again mitochondrion. biorxiv.org/content/10.110… Siewert-Jan Marrink Source code: github.com/weria-pezeshki…

Excited to introduce PyRoki ("Python Robot Kinematics"): easier IK, trajectory optimization, motion retargeting... with an open-source toolkit on both CPU and GPU

The ChimeraX 1.10 release candidate and daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer. rbvi.ucsf.edu/chimerax/data/…

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Boltz-2, released this morning, is now live on Rowan! All Rowan users can submit binding-affinity predictions through Rowan's web interface; we allocate cloud GPUs so calculations take just a few minutes. (It's free to make an account and try the new model out!)

We’re excited to introduce Chai-2, a major breakthrough in molecular design. Chai-2 enables zero-shot antibody discovery in a 24-well plate, exceeding previous SOTA by >100x. Thread👇

Someone on 🦋 shared a working AlphaFlow/ESMFlow colab notebook, I'll link it below 👇

After a 4-year journey, we are super happy to see this paper out in Nature Communications - Katarina Elez et al: High-throughput molecular dynamics + active machinelearning enable efficient identification of an experimentally-validated broad coronavirus inhibitor. nature.com/articles/s4146…