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Can Claude Code design proteins? We're just about to release our wet lab API + SDK so we made a quick demo to test how agents can interact with protein design models and submit the proteins to our lab for testing. This closes the loop between the computational design... show more

Julian Englert

2,822 subscribers

81,258 次观看 • 6 个月前 •via X (Twitter)

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🚀 Update! Our latest Pinal bioRxiv now includes wet lab results. More proteins with diverse text prompt on the way. Design proteins with just text. Everyone can do protein design! Demo: paper: GitHub:

🚀 Update! Our latest Pinal bioRxiv now includes wet lab results. More proteins with diverse text prompt on the way. Design proteins with just text. Everyone can do protein design! Demo: paper: GitHub:

fajie yuan

17,049 次观看 • 1 年前

The possibilities for AI-powered protein design are endless! In this case study we show how we used BindCraft to engineer a programmable maltose biosensor from scratch, including wet lab validation at Adaptyv of course. We envision a future where every biologist can make their own bespoke protein tools to investigate environmental samples, cell behaviour or create therapeutics. AI-based protein design can enable that future if powered by rapid wet lab validation. Once the cycle from design → test → application shrinks to weeks, the frontier explodes.

The possibilities for AI-powered protein design are endless! In this case study we show how we used BindCraft to engineer a programmable maltose biosensor from scratch, including wet lab validation at Adaptyv of course. We envision a future where every biologist can make their own bespoke protein tools to investigate environmental samples, cell behaviour or create therapeutics. AI-based protein design can enable that future if powered by rapid wet lab validation. Once the cycle from design → test → application shrinks to weeks, the frontier explodes.

Adaptyv Bio

52,115 次观看 • 11 个月前

“Proteins sticking to other proteins is what makes life exist.” 🧬 We explain the science behind AlphaProteo: our AI system for designing protein binders that holds huge potential for biology. ▶️ Hear from Jue Wang, co-lead of the protein design team, David La, research scientist, and Harshnira Patani, wet lab lead here at Google DeepMind. ↓

“Proteins sticking to other proteins is what makes life exist.” 🧬 We explain the science behind AlphaProteo: our AI system for designing protein binders that holds huge potential for biology. ▶️ Hear from Jue Wang, co-lead of the protein design team, David La, research scientist, and Harshnira Patani, wet lab lead here at Google DeepMind. ↓

Google DeepMind

67,570 次观看 • 1 年前

AI has solved software. Biology is the next frontier. We're hiring across every team at Adaptyv. We’ve built the best automated lab for protein designers to experimentally test their AI-designed proteins. Today, the most advanced protein design companies run their wet-lab work on Adaptyv, from the biggest biopharmas to frontier AI labs to dozens of virtual biotech startups. Demand has grown faster than we have, so we’re hiring across the board: • Bio: Research associates, scientists and lab technicians to develop and run new assays at scale. • Lab automation: Engineers and interns to onboard new lab instruments and scale our automation infrastructure. • Software: Product and backend engineers to scale LabOS, our internal lab orchestration platform, our API for agents and the data pipelines that turn messy physical-world data into clean results. • Partnerships, customer success and operations: Building partnerships with AI & pharma labs, making sure customers understand their data and can run more campaigns, making sure the company operations run smoothly

AI has solved software. Biology is the next frontier. We're hiring across every team at Adaptyv. We’ve built the best automated lab for protein designers to experimentally test their AI-designed proteins. Today, the most advanced protein design companies run their wet-lab work on Adaptyv, from the biggest biopharmas to frontier AI labs to dozens of virtual biotech startups. Demand has grown faster than we have, so we’re hiring across the board: • Bio: Research associates, scientists and lab technicians to develop and run new assays at scale. • Lab automation: Engineers and interns to onboard new lab instruments and scale our automation infrastructure. • Software: Product and backend engineers to scale LabOS, our internal lab orchestration platform, our API for agents and the data pipelines that turn messy physical-world data into clean results. • Partnerships, customer success and operations: Building partnerships with AI & pharma labs, making sure customers understand their data and can run more campaigns, making sure the company operations run smoothly

Adaptyv Bio

13,670 次观看 • 2 个月前

Another month, another insane protein design paper from the Baker Lab. This time: Designing binders for intrinsically disordered regions, a common & important component of proteins we care about, with the help of a diffusion model In nature last week

Another month, another insane protein design paper from the Baker Lab. This time: Designing binders for intrinsically disordered regions, a common & important component of proteins we care about, with the help of a diffusion model In nature last week

Julia Bauman

45,557 次观看 • 1 年前

What seemed like an intractable problem is now possible: To design proteins with a specified nonlinear mechanical response, capturing complex folding and unfolding mechanisms in singe and few-shot computations. We present ForceGen, an end-to-end algorithm for de novo protein generation based on nonlinear mechanical unfolding responses. Rooted in the physics of protein mechanics, this generative strategy provides a powerful way to design new proteins rapidly, including exquisite and rapid predictions about their dynamical behavior. Proteins, like any other mechanical object, respond to forces in peculiar ways. Think of the different response you'd get from pulling on a steel cable versus pulling on a rubber band, or the difference between honey and glass. Now, we can design proteins with a set of desirable mechanical characteristics, with applications from health to sustainable plastics. The key to solving this problem was to integrate a protein language model with denoising diffusion methods, and using accurate atomistic-level physical simulation data to endow the model a first-principles understanding. ForceGen can solve both forward and inverse tasks: In the forward task, we can predict how stable a protein is, how it will unfold and what the forces involved are, all given just the sequence of amino acids. In the inverse task, we can design new proteins that meet complex nonlinear mechanical signature targets. Read the paper, led by LAMM@MIT postdoc Bo Ni, published in Science Advances: Why do we care about the mechanics of proteins? The mechanics of proteins are critical elements of many living systems - as evidenced in many studies of mechanobiology. Through evolution, nature has presented a set of remarkable protein materials with unique mechanical functions like elastins, silks, keratins or collagens that play crucial roles in biology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. So far, the only way to do this was to use existing evolutionary concepts or to manually alter proteins. With our new generative model we can directly design proteins to meet complex nonlinear mechanical property-design objectives. ForceGen leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation from physical and chemical principles, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, and a detailed unfolding force-separation curves. ForceGen offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, to enable the discovery of new protein materials with superior mechanical properties. B. Ni, D.L. Kaplan, M.J. Buehler, ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model. Sci. Adv. 10, eadl4000 (2024). DOI: 10.1126/sciadv.adl4000 Codes and model weights available Hugging Face: David Kaplan

What seemed like an intractable problem is now possible: To design proteins with a specified nonlinear mechanical response, capturing complex folding and unfolding mechanisms in singe and few-shot computations. We present ForceGen, an end-to-end algorithm for de novo protein generation based on nonlinear mechanical unfolding responses. Rooted in the physics of protein mechanics, this generative strategy provides a powerful way to design new proteins rapidly, including exquisite and rapid predictions about their dynamical behavior. Proteins, like any other mechanical object, respond to forces in peculiar ways. Think of the different response you'd get from pulling on a steel cable versus pulling on a rubber band, or the difference between honey and glass. Now, we can design proteins with a set of desirable mechanical characteristics, with applications from health to sustainable plastics. The key to solving this problem was to integrate a protein language model with denoising diffusion methods, and using accurate atomistic-level physical simulation data to endow the model a first-principles understanding. ForceGen can solve both forward and inverse tasks: In the forward task, we can predict how stable a protein is, how it will unfold and what the forces involved are, all given just the sequence of amino acids. In the inverse task, we can design new proteins that meet complex nonlinear mechanical signature targets. Read the paper, led by LAMM@MIT postdoc Bo Ni, published in Science Advances: Why do we care about the mechanics of proteins? The mechanics of proteins are critical elements of many living systems - as evidenced in many studies of mechanobiology. Through evolution, nature has presented a set of remarkable protein materials with unique mechanical functions like elastins, silks, keratins or collagens that play crucial roles in biology. However, going beyond natural designs to discover proteins that meet specified mechanical properties remains challenging. So far, the only way to do this was to use existing evolutionary concepts or to manually alter proteins. With our new generative model we can directly design proteins to meet complex nonlinear mechanical property-design objectives. ForceGen leverages deep knowledge on protein sequences from a pretrained protein language model and maps mechanical unfolding responses to create proteins. Via full-atom molecular simulations for direct validation from physical and chemical principles, we demonstrate that the designed proteins are de novo, and fulfill the targeted mechanical properties, including unfolding energy and mechanical strength, and a detailed unfolding force-separation curves. ForceGen offers rapid pathways to explore the enormous mechanobiological protein sequence space unconstrained by biological synthesis, to enable the discovery of new protein materials with superior mechanical properties. B. Ni, D.L. Kaplan, M.J. Buehler, ForceGen: End-to-end de novo protein generation based on nonlinear mechanical unfolding responses using a language diffusion model. Sci. Adv. 10, eadl4000 (2024). DOI: 10.1126/sciadv.adl4000 Codes and model weights available Hugging Face: David Kaplan

Markus J. Buehler

47,242 次观看 • 2 年前

Today in nature we present the results of our exploration of the soluble protein universe and the design of functional soluble membrane proteins with Casper Goverde Nico Goldbach Bruno Correia 1/6

Today in nature we present the results of our exploration of the soluble protein universe and the design of functional soluble membrane proteins with Casper Goverde Nico Goldbach Bruno Correia 1/6

Martin Pacesa

138,470 次观看 • 2 年前

My lab, at Karolinska in Stockholm, is looking for a PhD student with a computational/quantitative background to work on probabilistic/generative models of protein (structure and sequence). The research will involve methods development and applications in vaccine design.

My lab, at Karolinska in Stockholm, is looking for a PhD student with a computational/quantitative background to work on probabilistic/generative models of protein (structure and sequence). The research will involve methods development and applications in vaccine design.

Ben Murrell

21,646 次观看 • 1 年前

NEW EPISODE of HARD DRUGS! AlphaFold, ProteinMPNN and other AI tools are transforming biology and drug design. But how do they work? What can’t they do (yet)? And can we use them to make a vaccine against Strep A for the very first time? In this episode, Jacob and I talk about hacking proteins with AI. 03:21 What makes proteins cool 05:29 Can we make a vaccine against Strep A? 10:12 Proteins in nature aren’t enough, and we can improve them with AI 21:12 ProteinMPNN and AlphaFold are transforming drug design 29:52 A short history of protein structure prediction from physical models to deep learning 34:48 Using AI to design a Strep A vaccine 39:27 Validating an AI-designed Strep A vaccine 43:09 Recent AI protein breakthroughs 49:30 Why we don’t already have a Strep A vaccine and the future of optimizing protein drugs

NEW EPISODE of HARD DRUGS! AlphaFold, ProteinMPNN and other AI tools are transforming biology and drug design. But how do they work? What can’t they do (yet)? And can we use them to make a vaccine against Strep A for the very first time? In this episode, Jacob and I talk about hacking proteins with AI. 03:21 What makes proteins cool 05:29 Can we make a vaccine against Strep A? 10:12 Proteins in nature aren’t enough, and we can improve them with AI 21:12 ProteinMPNN and AlphaFold are transforming drug design 29:52 A short history of protein structure prediction from physical models to deep learning 34:48 Using AI to design a Strep A vaccine 39:27 Validating an AI-designed Strep A vaccine 43:09 Recent AI protein breakthroughs 49:30 Why we don’t already have a Strep A vaccine and the future of optimizing protein drugs

Saloni

72,565 次观看 • 10 个月前

Proteins are the machinery of life. Scientists have cataloged billions of protein sequences—but their biology is still mostly unknown. Today we're releasing a world model of protein biology: a scientific engine for prediction, design, and discovery that consists of ESMFold2, ESMC, and ESM Atlas. Together, they're helping to open up a new way for researchers to design proteins and speed up scientific discovery. Our mission is to cure or prevent disease. To do that, we need to accelerate science. That's why we're releasing all three openly.

Proteins are the machinery of life. Scientists have cataloged billions of protein sequences—but their biology is still mostly unknown. Today we're releasing a world model of protein biology: a scientific engine for prediction, design, and discovery that consists of ESMFold2, ESMC, and ESM Atlas. Together, they're helping to open up a new way for researchers to design proteins and speed up scientific discovery. Our mission is to cure or prevent disease. To do that, we need to accelerate science. That's why we're releasing all three openly.

biohub

79,155 次观看 • 2 个月前

We're thrilled to present ESM3 in Science Magazine. ESM3 is a generative language model that reasons over the three fundamental properties of proteins: sequence, structure, and function. Today we're making ESM3 available free to researchers worldwide via the public beta of an API for biological intelligence. Trained with over a trillion teraflops of compute, this is the first time a model of this scale has been trained for biology, pushing the frontier of AI for biological discovery and engineering. ESM3 learns to represent the immense complexity of protein biology, learning from billions of natural proteins. From this training it developed the capability to design proteins, responding to complex prompts combining atomic level details and high level instructions to generate new proteins. ESM3 can explore protein space far beyond natural evolution. We prompted ESM3 to generate a fluorescent protein at a far distance from any known fluorescent proteins, searching an unknown region of protein space, to discover a new fluorescent protein. We estimate this is equivalent to simulating five hundred million years of evolution.

We're thrilled to present ESM3 in Science Magazine. ESM3 is a generative language model that reasons over the three fundamental properties of proteins: sequence, structure, and function. Today we're making ESM3 available free to researchers worldwide via the public beta of an API for biological intelligence. Trained with over a trillion teraflops of compute, this is the first time a model of this scale has been trained for biology, pushing the frontier of AI for biological discovery and engineering. ESM3 learns to represent the immense complexity of protein biology, learning from billions of natural proteins. From this training it developed the capability to design proteins, responding to complex prompts combining atomic level details and high level instructions to generate new proteins. ESM3 can explore protein space far beyond natural evolution. We prompted ESM3 to generate a fluorescent protein at a far distance from any known fluorescent proteins, searching an unknown region of protein space, to discover a new fluorescent protein. We estimate this is equivalent to simulating five hundred million years of evolution.

Alex Rives

227,379 次观看 • 1 年前

📢 We’re launching Proteina-Complexa — and after the Jensen keynote mention, we definitely had to post this thread now ;) Atomistic binder design with generative pretraining + test-time compute, plus large-scale wet-lab validation. Project page: 🧵 1/n

📢 We’re launching Proteina-Complexa — and after the Jensen keynote mention, we definitely had to post this thread now ;) Atomistic binder design with generative pretraining + test-time compute, plus large-scale wet-lab validation. Project page: 🧵 1/n

Kieran Didi

50,035 次观看 • 4 个月前

Today we're launching Latent-Y: the world's first autonomous agent for drug design, lab-validated end to end. Give it a research goal. Latent-Y reasons, designs, iterates, and delivers lab-ready antibodies, autonomously or collaboratively, with the biological reasoning of a PhD protein design expert. Technical report: Blog post: Apply for access:

Today we're launching Latent-Y: the world's first autonomous agent for drug design, lab-validated end to end. Give it a research goal. Latent-Y reasons, designs, iterates, and delivers lab-ready antibodies, autonomously or collaboratively, with the biological reasoning of a PhD protein design expert. Technical report: Blog post: Apply for access:

Simon Kohl

121,173 次观看 • 4 个月前

A visual design experiment built on Replit ⠕. UIs in sci-fi movies were the inspiration. A galactic radar listening for signals across the stars with simulated data. Designed to test how far design and code can merge into something beautiful. See it for yourself:

A visual design experiment built on Replit ⠕. UIs in sci-fi movies were the inspiration. A galactic radar listening for signals across the stars with simulated data. Designed to test how far design and code can merge into something beautiful. See it for yourself:

Levin Stanley

294,007 次观看 • 9 个月前

Automating the lab bench is the best thing we can do for AI in biology. Most experiments are still run by hand. Every biologist's handiwork is unique and every lab is a little different. So, biology faces widespread reproducibility issues. But, AI will demand more reproducible data than we can produce, and generate more ideas than we can test. Experiments must be communicated and executed in a standardized way to generate reproducible data. So, Tetsuwan is building a lab where users specify experiments in an exact syntax. These experiments are executed by an automated platform to generate transparent, reproducible output. The user never needs physical access to a lab. This is a biology lab you can use like a computer. Our platform, built and tested with pilot labs over the past two years, lets users configure automated workflows rapidly & precisely. Later this year, we will bring our first services online, focusing on functional screens for protein design. Alex and I met at Caltech, where she was one year my senior. We're building this company because we were little kids who wanted to be biologists that grew up into adults who resented the lab bench. We want biology to be about asking questions, not the painful and frustrating manual process of asking them. For those looking to receive updates on our pilot services, looking for a meaningful job, or just to learn more about our work, see the links in the comments!

Automating the lab bench is the best thing we can do for AI in biology. Most experiments are still run by hand. Every biologist's handiwork is unique and every lab is a little different. So, biology faces widespread reproducibility issues. But, AI will demand more reproducible data than we can produce, and generate more ideas than we can test. Experiments must be communicated and executed in a standardized way to generate reproducible data. So, Tetsuwan is building a lab where users specify experiments in an exact syntax. These experiments are executed by an automated platform to generate transparent, reproducible output. The user never needs physical access to a lab. This is a biology lab you can use like a computer. Our platform, built and tested with pilot labs over the past two years, lets users configure automated workflows rapidly & precisely. Later this year, we will bring our first services online, focusing on functional screens for protein design. Alex and I met at Caltech, where she was one year my senior. We're building this company because we were little kids who wanted to be biologists that grew up into adults who resented the lab bench. We want biology to be about asking questions, not the painful and frustrating manual process of asking them. For those looking to receive updates on our pilot services, looking for a meaningful job, or just to learn more about our work, see the links in the comments!

Cristian Ponce

839,971 次观看 • 1 个月前

We connected our autonomous lab to OpenAI's GPT-5 and let it run 36,000 experiments. The result was a new state-of-the-art for Cell-Free Protein Synthesis that cut costs by 40% per gram of protein. You can now order the beta version for your own lab: You can read the full preprint and read OpenAI’s blog post about our work here: See the full press release here:

We connected our autonomous lab to OpenAI's GPT-5 and let it run 36,000 experiments. The result was a new state-of-the-art for Cell-Free Protein Synthesis that cut costs by 40% per gram of protein. You can now order the beta version for your own lab: You can read the full preprint and read OpenAI’s blog post about our work here: See the full press release here:

Ginkgo Bioworks

80,501 次观看 • 6 个月前

Demo 2: human + agent design loop inside Codex. Not every workflow needs the agent to drive everything. You design in Open Design. Codex reviews the output. It can inspect files, open pages, test interactions, critique the design, and turn feedback into the next prompt. Design becomes a human + agent feedback loop.

Demo 2: human + agent design loop inside Codex. Not every workflow needs the agent to drive everything. You design in Open Design. Codex reviews the output. It can inspect files, open pages, test interactions, critique the design, and turn feedback into the next prompt. Design becomes a human + agent feedback loop.

Open Design

20,103 次观看 • 2 个月前

Everyone is obsessed with 🦞 OpenClaw🦞 and moltbook and the idea of autonomous agents running your life or building societies. But what happens when you scale that up? What if, instead of agents checking your calendar and posting on Reddit, you had hundreds of agents collaborating to construct the building blocks of life 🧬 from "first principles"? We created a Swarm of AIs to design never-before-seen-proteins, far outside of what Nature has produced. They negotiate, debate, and optimize locally to design proteins from scratch, with decentralized logic. No training required, pure emergence! These proteins 👇 were designed by a swarm of AIs!

Everyone is obsessed with 🦞 OpenClaw🦞 and moltbook and the idea of autonomous agents running your life or building societies. But what happens when you scale that up? What if, instead of agents checking your calendar and posting on Reddit, you had hundreds of agents collaborating to construct the building blocks of life 🧬 from "first principles"? We created a Swarm of AIs to design never-before-seen-proteins, far outside of what Nature has produced. They negotiate, debate, and optimize locally to design proteins from scratch, with decentralized logic. No training required, pure emergence! These proteins 👇 were designed by a swarm of AIs!

Markus J. Buehler

72,672 次观看 • 6 个月前

For years, the design industry has talked about "design vs code" And tools (including Figma!) have forced a choice. But this is a false debate. Code isn't the opposite of design. Code is a material for design. So we're bringing code to the Figma canvas with Code Layers.

For years, the design industry has talked about "design vs code" And tools (including Figma!) have forced a choice. But this is a false debate. Code isn't the opposite of design. Code is a material for design. So we're bringing code to the Figma canvas with Code Layers.

Dylan Field

96,942 次观看 • 1 个月前

”David Baker, Demis Hassabis and John Jumper, your ground-breaking work in computational protein design and protein structure prediction has revolutionised these fields. It has opened up completely new possibilities to design proteins that have never been seen before, and we now have access to predicted structures of all 200 million known proteins. These are truly great achievements.” Watch the very moment the chemistry laureates received their Nobel Prize diplomas and medals during the 2024 Nobel Prize award ceremony. #NobelPrize

”David Baker, Demis Hassabis and John Jumper, your ground-breaking work in computational protein design and protein structure prediction has revolutionised these fields. It has opened up completely new possibilities to design proteins that have never been seen before, and we now have access to predicted structures of all 200 million known proteins. These are truly great achievements.” Watch the very moment the chemistry laureates received their Nobel Prize diplomas and medals during the 2024 Nobel Prize award ceremony. #NobelPrize

The Nobel Prize

295,241 次观看 • 1 年前