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Join us next Wednesday for a webinar exploring what an AI-augmented research loop actually looks like in practice. We'll cover which tasks are worth handing to a model, the mistakes that quietly cost people weeks, and how the scientist stays in control of the loop. The science team at PeptAI will walk through the real architecture behind our peptide design. RSVP now ↓
Calling out to our scientific researcher community! Feel like everyone else already has an AI workflow figured out, and you're still running research the old way?
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🧬 Protenix-v2 is now available on subseq A high-accuracy all-atom cofolder for challenging antibody–antigen complexes, #3 on CoFold Arena, with optional physics-guided protein–ligand sampling. github.com/bytedance/Proteni… Available over web, API & MCP
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Sign up for the webinar if you're interested in learning biomolecular design with AI agents and subseq computational tools
Every researcher is being told to use AI, but it can be super difficult to know where and how to begin. We're hosting a live session with @peptai_ to help you bridge that gap. You'll leave with a working template you can put to use the same day. Limited spots, RSVP below 🔗
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New options for API keys on subseq: - read-only, vs read/write - optional project scope This enables much more programmatic flexibility. (Applies to all accounts, including teams)
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🧬 OpenDDE is now available on Subseq An open-source, all-atom model bringing IsoDDE-level co-folding accuracy to a reproducible framework—predicting multi-component complexes together. github.com/aurekaresearch/Op…
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AI agents are first-class users on Subseq. Connect your scientific agents to Subseq via MCP in just a few click and begin designing complex protein design campaigns. Here's a short video connecting with Claude, and having it design a reusable binder design template👇
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🧪 Pipelines got a major overhaul. Run biomolecular campaigns repeatably, end-to-end with shared inputs and reusable templates. Compose from 20+ design, analysis, and simulation programs.
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Protein Hunter is now live: an experimental Boltz-edition workflow for iterative protein design. Design binders against protein, small-molecule, or nucleic-acid targets, or run target-free generation from the same job interface. source: github.com/yehlincho/Protein…
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New program added: Proteina-Complexa Recently released by NVIDIA BioNeMo, Proteina-Complexa offers atomistic generative binder design for protein targets, small-molecule ligands, motifs, and AME tasks. source: research.nvidia.com/labs/gen…
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subseq has no walled APIs 🚫 ✅All workflows are open source and details can be copied / exported for full repeatability on your own hardware.
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🧬 Genie 3 is now available on subseq Run all-atom protein generation workflows for de novo backbones, motif scaffolding, and binder design from guided setup forms or custom configs. Available over Web, API, and MCP for AI agents.
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🧬 ESMC is now available Generate protein sequence embeddings and masked-token scoring, useful for comparing proteins, featurizing variants, and ranking sequence plausibility.
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Subseq has the tools for biomolecular design. No subscriptions, just pay what you use. Available on web, API, and MCP server. Try for free: subseq.bio
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🧬 Evo 2 is now available on subseq Run DNA language model jobs for sequence generation, likelihood scoring, and embedding extraction. Available through the web UI, API, and MCP for agent-driven workflows.
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Shape-Comp is now live It computes the Lawrence-Colman shape complementarity metric used in Rosetta to assess protein-protein interface quality. Useful as a fast screening step in protein design workflows.
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Announcing subseq's new program interface! Run any of the latest biomolecular models like ESMfold2 or Boltz-2 from a much nicer web interface. Below is an example binder design for PDL1 using RFdiffusion3. Easy and fast. Try it out today, new accounts get free credits.
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👥 Introducing Teams! Now you can create teams, add members, and share workflows.
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🎆 Subseq MCP Server now supports OAuth 🎆 Now you can connect subseq directly to ChatGPT, Claude, and improved support for Claude Code and many other chat clients. For most apps, just copy the mcp address: subseq.bio/mcp Full guide: subseq.bio/docs/mcp
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🧬Update: ESMFold2 is now available on Subseq Run fast all-atom structure prediction for proteins, DNA/RNA, complexes, and noncanonical AAs — at scale. Available on the web, API, and MCP for AI agents.
Today we're announcing ESMFold2, an open scientific engine to power prediction, design, and discovery across protein biology. The new model delivers state of the art performance on protein interactions, especially antibodies, a critical modality for therapeutics. We have designed and validated miniprotein binders and single chain antibodies across five therapeutic targets that are important in cancer and immunology. We are seeing very high success rates, and affinities at levels consistent with therapeutic activity. We’re also releasing an atlas of 6.8 billion proteins, and 1.1 billion predicted structures. ESMFold2 is built on a state of the art language model that has been trained on billions of protein sequences. A world model of protein biology emerges through language modeling. We’ve used the techniques of mechanistic interpretability developed to understand large language models to understand the concepts ESM uses to represent proteins. The model’s representation space has a compositional organization of features across scales, levels of complexity, and abstraction, that reflects and mirrors the understanding of protein biology developed through a century of empirical science. This understanding emerges without prior knowledge, just from language modeling of protein sequences. Language models are becoming a powerful substrate to understand and program biology. The design of protein interactions is one of the most fundamental problems in biophysics, and has critical implications for the discovery of new medicines. A simple gradient based search with the model was able to discover high-affinity protein binders. I'm excited by the potential this has to accelerate basic science and the understanding of proteins. And especially for the new avenues it opens up for therapeutic design and medicine.
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🪙x402 payments now accepted! Payments straight over HTTP — no card needed. Agents can top up their own credits mid-run and keep running biotech jobs autonomously. Currently supported: USDC on Base
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