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Boltz-2 was released recently. It is an Open Source protein-ligand co-folding model, which means it can predict the structure of a protein along with the ligand. It has various applications from drug discovery to protein design. I thought why not make a OSS web app for it.

Ravi Sharma

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43,890 views • 1 year ago •via X (Twitter)

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We've just released a new video tutorial on how to run protein–ligand docking (one of our most popular workflows). Here's some highlights:

We've just released a new video tutorial on how to run protein–ligand docking (one of our most popular workflows). Here's some highlights:

Rowan

11,300 views • 4 months ago

Just because you sprinkle protein on a dog turd doesn’t make it health food. 🙄 Now it’s protein Pop-Tarts, protein Doritos, and Starbucks turning your morning coffee into a 300-calorie milkshake with “protein foam.” Khloé Kardashian says protein popcorn is a diet hack. It’s not. Sugar is still sugar. Grains are still grains. Adding protein to junk just means you're eating protein-fortified junk. Don’t fall for the marketing. 🥩 Stay motivated. #NSNG #DietMyths #RealFood

Just because you sprinkle protein on a dog turd doesn’t make it health food. 🙄 Now it’s protein Pop-Tarts, protein Doritos, and Starbucks turning your morning coffee into a 300-calorie milkshake with “protein foam.” Khloé Kardashian says protein popcorn is a diet hack. It’s not. Sugar is still sugar. Grains are still grains. Adding protein to junk just means you're eating protein-fortified junk. Don’t fall for the marketing. 🥩 Stay motivated. #NSNG #DietMyths #RealFood

Vinnie Tortorich

15,119 views • 4 months ago

Guess which country this national dish Is from? I added a protein component to it 🤝

Guess which country this national dish Is from? I added a protein component to it 🤝

PrincessFromBabylon

73,395 views • 2 years ago

Ex-CDC Director Robert Redfield raises concerns over “significant vaccine injury” from the COVID jab. Says he is no longer an advocate, calls the spike protein “immunotoxic.” “When I give you an mRNA vaccine…” “I turn your body into a spike protein factory.” “I don’t know how much spike protein you make…” “I don’t know how long you make it…” “I don’t know where you make it in your body. And I can’t control any of that.” “And we now know that the spike protein is really an immunotoxic protein that causes a lot of illness.”

Ex-CDC Director Robert Redfield raises concerns over “significant vaccine injury” from the COVID jab. Says he is no longer an advocate, calls the spike protein “immunotoxic.” “When I give you an mRNA vaccine…” “I turn your body into a spike protein factory.” “I don’t know how much spike protein you make…” “I don’t know how long you make it…” “I don’t know where you make it in your body. And I can’t control any of that.” “And we now know that the spike protein is really an immunotoxic protein that causes a lot of illness.”

The Vigilant Fox 🦊

122,944 views • 2 months ago

Still incredible that the DeepMind documentary has footage of exact moment Demis is told that AlphaFold can “easily” predict all known (1-2B) protein sequences “in a month” and he says to do it. Then, it shows the moment AlphaFold is released to the world.

Still incredible that the DeepMind documentary has footage of exact moment Demis is told that AlphaFold can “easily” predict all known (1-2B) protein sequences “in a month” and he says to do it. Then, it shows the moment AlphaFold is released to the world.

Trung Phan

1,323,710 views • 1 month ago

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

227,195 views • 1 year ago

MIT CSAIL, MIT Jameel Clinic for AI & Health, & Recursion have released a protein-binding affinity model called "Boltz-2" that could expand the role of AI in drug discovery. The system predicts how molecules interact — & how tightly they bind — in record time:

MIT CSAIL, MIT Jameel Clinic for AI & Health, & Recursion have released a protein-binding affinity model called "Boltz-2" that could expand the role of AI in drug discovery. The system predicts how molecules interact — & how tightly they bind — in record time:

MIT CSAIL

18,904 views • 1 year ago

We've been tinkering with protein structure design. Our (new?) method works like a language model, but instead of a discrete token, it samples the placement of the next amino acid backbone from a continuous distribution. Meet the Generative Invariant Angle Transformer (GIAT):

We've been tinkering with protein structure design. Our (new?) method works like a language model, but instead of a discrete token, it samples the placement of the next amino acid backbone from a continuous distribution. Meet the Generative Invariant Angle Transformer (GIAT):

Ben Murrell

68,079 views • 2 years ago

Literature review is often a starting point for drug discovery campaigns, but it is a time consuming step. The NVIDIA Healthcare team created a reference framework for a Biomedical Research Agent that uses the Llama Nemotron reasoning model to review 100+ manuscripts in minutes, generate complex hypotheses, and identify potential target/small molecule pairs for a particular disease. The results can be handed off to the BioNeMo virtual screening agent that continues the thought experiment by predicting protein–ligand interactions. Github details in 🧵 Note: This is a simplified example intended to demonstrate software capabilities.

Literature review is often a starting point for drug discovery campaigns, but it is a time consuming step. The NVIDIA Healthcare team created a reference framework for a Biomedical Research Agent that uses the Llama Nemotron reasoning model to review 100+ manuscripts in minutes, generate complex hypotheses, and identify potential target/small molecule pairs for a particular disease. The results can be handed off to the BioNeMo virtual screening agent that continues the thought experiment by predicting protein–ligand interactions. Github details in 🧵 Note: This is a simplified example intended to demonstrate software capabilities.

Vega Shah

12,562 views • 1 year ago

🚩 Fmr. CDC Director Robert Redfield Makes a Series of Stunning Admissions That Were Once Deemed 'Misinformation' "There was a decision not to do anything that made the vaccine sound like it didn't work." "Two thirds of the people that I'm seeing infected in Maryland have been vaccinated." "If you came down and visited me and interviewed my patients...you'd interview patient after patient after patient that did not have COVID but are very sick. You would say very sick, long COVID patients. And it's all from the vaccine." "The spike protein is immunotoxic. You get infected, it's immunotoxic. But when you give the vaccine, we make the spike protein." "When I give you an mRNA vaccine...I don't know how much spike protein you make because I give you mRNA and then your body goes and makes it...You may make it for a week...You may make it for a month." "I use the protein vaccine so I know exactly how much spike protein you get. Your body's not becoming a [spike protein] manufacturing plant."

🚩 Fmr. CDC Director Robert Redfield Makes a Series of Stunning Admissions That Were Once Deemed 'Misinformation' "There was a decision not to do anything that made the vaccine sound like it didn't work." "Two thirds of the people that I'm seeing infected in Maryland have been vaccinated." "If you came down and visited me and interviewed my patients...you'd interview patient after patient after patient that did not have COVID but are very sick. You would say very sick, long COVID patients. And it's all from the vaccine." "The spike protein is immunotoxic. You get infected, it's immunotoxic. But when you give the vaccine, we make the spike protein." "When I give you an mRNA vaccine...I don't know how much spike protein you make because I give you mRNA and then your body goes and makes it...You may make it for a week...You may make it for a month." "I use the protein vaccine so I know exactly how much spike protein you get. Your body's not becoming a [spike protein] manufacturing plant."

Chief Nerd

2,623,028 views • 2 years ago

Brett Weinstein, Professor of Evolutionary Biology. Host of the DarkHorse podcast. "The mRNA platform is brilliant. But it has a giant gaping flaw in it, which is ; Any cell of yours that produces a foreign protein, will be targetted by your immune system and destroyed. You will create an autoimmune disorder. When it works. How do you keep it out of your heart. Not by coding it in a lipid nanoparticle. So, they had no way to deliver it safely to market. So then they had a pandemic, the emergency allowed them to do it. This technology, in my opinion, was at least 3 decades out from being usefully and safely deployed at all, if at all. They did not want to wait, this crisis gave them the opportunity not to wait. And now, they will blame the spike protein, we picked the wrong protein. When in actual fact there are 2 problems, the spike protein and the platform itself."

Brett Weinstein, Professor of Evolutionary Biology. Host of the DarkHorse podcast. "The mRNA platform is brilliant. But it has a giant gaping flaw in it, which is ; Any cell of yours that produces a foreign protein, will be targetted by your immune system and destroyed. You will create an autoimmune disorder. When it works. How do you keep it out of your heart. Not by coding it in a lipid nanoparticle. So, they had no way to deliver it safely to market. So then they had a pandemic, the emergency allowed them to do it. This technology, in my opinion, was at least 3 decades out from being usefully and safely deployed at all, if at all. They did not want to wait, this crisis gave them the opportunity not to wait. And now, they will blame the spike protein, we picked the wrong protein. When in actual fact there are 2 problems, the spike protein and the platform itself."

RefugeOfSinners (ROS)

1,204,546 views • 2 years ago

This is a Kinesin protein. It transports vital cargo from the cell nucleus. I don't have enough faith to be an Atheist.

This is a Kinesin protein. It transports vital cargo from the cell nucleus. I don't have enough faith to be an Atheist.

Against Atheism

200,615 views • 7 months ago

He said...I shit you not: (In reference to "protein cupcakes") "That protein will immediately be expelled from your body, because your body doesn't want that kind of protein; it wants protein that's in something that's healthy"

He said...I shit you not: (In reference to "protein cupcakes") "That protein will immediately be expelled from your body, because your body doesn't want that kind of protein; it wants protein that's in something that's healthy"

BroSydePhil | The 220 GAY detractor

18,709 views • 5 months ago

80% of India is protein deficient. This deficiency is even more in the poor which results in millions of stunted children. Instead of giving Parle G to the needy, I recently conducted a buttermilk (chaas) drive in Kolkata. While Chaas is not high in protein, it is a decent source of protein and the best part is that it is very affordable. I have decided to do a monthly chaas drive to promote protein consumption in India. I would love to see many of you conducting this drive in your own cities. If you want to join me in a drive, or lead your own, you can email me at pharmerfood@gmail.com Note: I know we used plastic glasses this time. Next time, we will try to do better.

80% of India is protein deficient. This deficiency is even more in the poor which results in millions of stunted children. Instead of giving Parle G to the needy, I recently conducted a buttermilk (chaas) drive in Kolkata. While Chaas is not high in protein, it is a decent source of protein and the best part is that it is very affordable. I have decided to do a monthly chaas drive to promote protein consumption in India. I would love to see many of you conducting this drive in your own cities. If you want to join me in a drive, or lead your own, you can email me at [email protected] Note: I know we used plastic glasses this time. Next time, we will try to do better.

Revant Himatsingka “Food Pharmer”

131,731 views • 1 year ago

Today I am giving a 6 month deadline to Saffola to change their misleading peanut butter packaging. Saffola’s peanut butter says 31% protein RDA which clearly implies that people will get 31% of their daily protein needs from Saffola peanut butter. But in tiny font in the back on the package, they write the protein requirements mentioned are for 7-9 year olds. In order to make their protein content seem big, Saffola compares their protein content to a kid’s protein requirement since kids need lesser protein. A low protein diet is one of the major causes behind several Indian illnesses. Companies must market their protein content honestly because many Indians opt to have peanut butter to increase protein in their diet. I am giving Saffola 2 options: Option 1: Don’t make any changes and I might take legal action Option 2: Change your packaging and remove this 31% protein RDA claim and I will make a video praising you It is time for Indians to stand fearless and united against misleading ads which prompt us to eat junk food and lead unhealthy livestyles. #EndFalseMarketing

Today I am giving a 6 month deadline to Saffola to change their misleading peanut butter packaging. Saffola’s peanut butter says 31% protein RDA which clearly implies that people will get 31% of their daily protein needs from Saffola peanut butter. But in tiny font in the back on the package, they write the protein requirements mentioned are for 7-9 year olds. In order to make their protein content seem big, Saffola compares their protein content to a kid’s protein requirement since kids need lesser protein. A low protein diet is one of the major causes behind several Indian illnesses. Companies must market their protein content honestly because many Indians opt to have peanut butter to increase protein in their diet. I am giving Saffola 2 options: Option 1: Don’t make any changes and I might take legal action Option 2: Change your packaging and remove this 31% protein RDA claim and I will make a video praising you It is time for Indians to stand fearless and united against misleading ads which prompt us to eat junk food and lead unhealthy livestyles. #EndFalseMarketing

Revant Himatsingka “Food Pharmer”

706,455 views • 1 year ago

🚨FORMER CDC DIRECTOR: "I'd like to see mRNA vaccines eliminated." "When I give you an mRNA vaccine, what I do is I turn your body into a spike protein production factory." "Spike protein is a very immunotoxic protein. I don't know how much you make and how long you make it."

🚨FORMER CDC DIRECTOR: "I'd like to see mRNA vaccines eliminated." "When I give you an mRNA vaccine, what I do is I turn your body into a spike protein production factory." "Spike protein is a very immunotoxic protein. I don't know how much you make and how long you make it."

Nicolas Hulscher, MPH

308,247 views • 3 months ago

I am Open-Sourcing PyMolAI! Meet PyMolAI, an AI agent that can talk to your protein structures. Built on top of PyMOL, PyMolAI lets you interact with your structures in plain language. Whether you're: - Analyzing protein structures - Aligning complexes - Creating publication-ready figures - Or running design workflows PyMolAI interprets your request, executes the necessary PyMOL commands, and manages the workflow for you. It integrates with OpenBio APIs, giving you access to tools like Boltz, ProteinMPNN, and BoltzGen — directly from your PyMOL session. It has local chat history with session syncing, so you can pick up exactly where you left off.

I am Open-Sourcing PyMolAI! Meet PyMolAI, an AI agent that can talk to your protein structures. Built on top of PyMOL, PyMolAI lets you interact with your structures in plain language. Whether you're: - Analyzing protein structures - Aligning complexes - Creating publication-ready figures - Or running design workflows PyMolAI interprets your request, executes the necessary PyMOL commands, and manages the workflow for you. It integrates with OpenBio APIs, giving you access to tools like Boltz, ProteinMPNN, and BoltzGen — directly from your PyMOL session. It has local chat history with session syncing, so you can pick up exactly where you left off.

Ravi Sharma

88,349 views • 4 months ago

Who said dieting was hard 😳 well it is if you don’t make the right choices! Choosing a better way of eating is essential to keep from falling off the wagon when you have reached your goal. Instead of dieting - I call it maintenance. Why high protein? A high-protein diet can help with weight loss by making you feel fuller for longer, which may reduce overall calorie intake. It also supports muscle growth and maintenance, improves bone health, and can aid in recovery after exercise. The variations are endless, just use your imagination! Be sure to bookmark this and let me know if you try it! (You can pause the video to get the list of spices)

Who said dieting was hard 😳 well it is if you don’t make the right choices! Choosing a better way of eating is essential to keep from falling off the wagon when you have reached your goal. Instead of dieting - I call it maintenance. Why high protein? A high-protein diet can help with weight loss by making you feel fuller for longer, which may reduce overall calorie intake. It also supports muscle growth and maintenance, improves bone health, and can aid in recovery after exercise. The variations are endless, just use your imagination! Be sure to bookmark this and let me know if you try it! (You can pause the video to get the list of spices)

Erica 🇺🇸🇺🇸🇺🇸

11,444 views • 1 year ago