subseq.bio

🪅Update: OpenFold-3 is now available on subseq! "OpenFold3-preview is a biomolecular structure prediction model aiming to be a bitwise reproduction of DeepMind's AlphaFold3" Source: github.com/aqlaboratory/o… This marks the 18th, and 5th structure prediction, program on subseq.

🧩 Introducing: Templates! Now you can save and load JSON templates for any number of complex job pipelines, including customizable variables. This simplifies multi-step pipelines into a set of variables, making for easy re-usability. Here is a demo for a 5-step template.

🔮BioEmu is now available! BioEmu is a generative protein “dynamics” model that rapidly samples realistic conformational ensembles for a given protein. source: github.com/microsoft/bioe… Try it at subseq.bio, with many other pre-configured protein design programs.

🎊 Chai-1 is now available! A fast, all-atom complex structure predictor, including restraint specification. (Source: github.com/chaidiscovery/…) Try it out at subseq.bio

✍️ Update! Now you can edit data directly in the browser. Currently text-based files supported.

New icons and collapsible nav bar give more space for protein design.

end-to-end jobs*

🏭Introducing Pipelines Submit a series of end-to-end from a single spec. Use the Pipeline Builder on the UI to construct multi-step jobs, with automatic data routing. Save or upload pipeline JSON for reusing favorite job steps. Available on UI + API.

🗞️New Project Viewer! A new UI page lets you see all assets associated with a project for better organization.

📰Introducing subseq Blog! subseq.bio/blog First blog post: Intro to GROMACS for Protein Design subseq.bio/blog/intro-to-…

📃New MCP docs: subseq.bio/docs/mcp

🔗New: Pre-signed URL's allow for quick sharing of datasets, jobs, or any individual file within them. Anyone with the links can download the data within the expiration window. Available on Web, API, and MCP tools.

c7 symmetric diffusion in action, unconditional backbones. One-shotted with codex using @subseqbio rfdiffusion -> pymol+

A year ago today I launched @subseqbio — a minimal protein design service, offering rfdiffusion and alphafold, pre-configured in a simple UI. Today it's a growing toolkit with many more program types: diffusion (RFdiffusion3, BoltzGen), docking, MD, alignment, seq prediction, and more. What’s new since then: - Job output-to-input routing. - Full API for custom end-to-end pipelines - In-browser viewers for fast sanity checks - MCP server for AI agents (!) 🤖 Built around commercially-permissive tools, versions and logs make for easy reproducibility. Simple credit-based runtime pricing, no subscriptions. (Free credits on sign-in until end of year.) I’m convinced protein design is a paradigm shift — and looking forward to making the service more useful. 🚀 Feedback + feature requests are welcome!

⚡️Subseq MCP Server is now live! ⚡️ Server: subseq.bio/mcp Requires: Authorization: Bearer <SUBSEQ_API_KEY> or set SUBSEQ_API_KEY env var.

✅Update: job logs now show tail of rolling output. Can now view the logs during long job runs. 📜

📡Update: Boltz-2 is now available on subseq This includes both boltz-1 and boltz-2 models. github.com/jwohlwend/boltz

🎇RFdiffusion3 is now available on subseq.bio ! RFdiffusion3 (RFD3) is a diffusion method that can design protein structures under complex constraints.

🎀Holiday Promo: Activated🎀 Until end of year, all new signups on subseq.bio will be given $5.00 in free, non-expiring credits! Try out any of the programs offered, enough for hours of runtime, such as BoltzGen, RFdiffusion, Alphafold, and more. #Biotech

⚡️Update: DiffDock-PP has been added! DiffDock-PP is a diffusion-based tool for protein-protein docking: given two protein structures, it translates and rotates them into ranked likely bound complexes. github.com/ketatam/DiffDo…