DeepMind AlphaFold 3 - This Will Change Everything!
ฝัง
- เผยแพร่เมื่อ 7 พ.ค. 2024
- 📝 Check out AlphaFold 3 here:
dpmd.ai/yt-tmp-alphafold3
📝 Or try it out through AlphaFold server for free:
alphafoldserver.com/
This video was made in partnership with Google DeepMind.
My paper on simulations that look almost like reality is available for free here:
rdcu.be/cWPfD
Or this is the orig. Nature Physics link with clickable citations:
www.nature.com/articles/s4156...
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#AlphaFold3 #AlphaFold - วิทยาศาสตร์และเทคโนโลยี
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Alphafold changed bìotechnology forever. This is huge! Looking forward to working with the new version
Could it be also used as "chemtrails" to "eat" CO2 from the atmosphere to transform it into a harmless gas?
@@Z0MBUSTER God designed molecular nanomachines to do that, it's called photosynthesis❗
No human involvement needed. If we have twice the Co2 in the air one day, plants will grow twice as fast.
Co2 is a harmless gas --- and we would die without it. Don't believe the propaganda. Historically, Co2 levels have been much higher in the far past. ❗❗❗❗❗❗
We have done this foldingathome using gpu since 2002... hardforums team, especially. We used to teach people how to do it at home, long before bitcoin mining using gpu, which we did back when bitcoins were useless except to other bitcoiners.
@@Z0MBUSTER co2 is not the issue, its methane... many commercial growers ON TH-cam dump co2 into grow areas, and a lot of it escapes. Methane from factories and smog byproducts is far worse....and a major concern, which breaks down into more co2, ironically.. you can capture it in a balloon shape object, and power generators. Methane is 28x worse greenhouse gas than co2.
@@Z0MBUSTERone big problem with this kind of climate engineering is that it's hard to predict what long term side-effects it can have. I imagine that the plastic-digesting example can't be used outside of highly controlled environments.
I wasn’t impressed until I heard AlphaFold had implemented Dark Mode. What a time to be alive!
I was literally about to make a joke lol
I've been waiting for BOINC to add dark mode for a while😂
"Dark Reader" extension for browser (free)
fairly big reason for why I've been using mostly linux since the 90s was inability to control blinding background colors in other OSes. now 20+ years later windows11 and macos are finally able to display most window contents with dark background, it was a pretty momentous achievement (their highly paid UI/usability "experts" are idiots)
Just imagine where we'll be just two papers down the line!
4 minutes earlier than the official Google deepmind channel? That was indeed fast, you're right
🙂
TwoMinutePapers be like: *sniffs white substance*, "lets read these papers!"
@@JohnDontFollowMe I think our man needs the white substance to get *down* after reading a really good paper.
@@JohnDontFollowMe 2MP needs not the "white substance".
Bro Fahir has the spice melange..... he IS the Kwisatz Haderach! 😁
Stuff like this saving lives is why i am going to study artificial intelligence when im out of highschool
This really made my day. Thank you so much! 🙏
Artificial intelligence will study YOU!
you could already begin studying it! I started learning how to program even before high-school , and I now realize that although I didn't have a real clue of what I was doing back then, it actually helps a lot to already be in the water 😃
Why wait?! 🙂 A good grounding in high school maths will get you a long way in AI
This is where you learn to be a wizard, Harry! (PS: Ignore the trolls under the bridge, concentrate on your studies).
Version 4 can fold your laundry. Version 5 can cut onions without crying.
version 6 can out-pizza the hut
Wearing contacts keeps you from crying over dead onions
Version 8 will get the fusion reactor going,,,
This is Nobel prize, Turing award level work and “Dark mode!” Life is strange.
well you don't award those until after the chickens hatch then you count them.
Dark Mode alone is enough for a Nobel Prize
What a time to hold on to my papers
I'm around 50 now and seeing that the field I love is doing real change (not in a "generating revenue" way, but in actual "improving humankind" way) brings a tear to my eye. Maybe a 20-something years old kid does not realize how big this is, but for me it is, truly and marvelously, an amazing time to be alive. Gives me a bit of hope that before I kick the bucket I'll get to see some of that utopian advancement and eradication of diseases we used to dream about.
I am 30 ad I too am amaized. I remember reading SCI-Fi books where we were able to simulate proteins and their interaction. And you could give a cancer genome to the computer and it would give you a blueprint for protein that is poisonous to the cancer, but not to the host. (So like a perfect cancer treatment, you just had to drink/inject the "poison" :D)
And now I might live to see something like that come to life.
@@_sky_3123 I'm 66 :-) Need I say more? I hope I can extend my time being alive.
Could it fix Long Covid please? I'm less than a bit alive at the moment, I'm after quality rather than length, but I'll be happy with both !
What could be a scenario that you could imagine happening now after this? And when? :)
20 smth college grads are developing AI lol
I'm 45 and hope that this means that our generation will not have to endure the chronic illnesses of old age that plagued our grandparents and are hitting our parents now. Maybe this means Alzheimer's and dementia will not end up costing TRIPLE what it currently does by 2050, which it will according to current predictions. And maybe even reverse aging to some extent.
AlphaFold - 2018. AlphaFold 2 - 2020. AlphaFold 3 - 2024. Nobody saw anyo of this coming a whole _six years ago._Who even knows what's coming now.
ChatGPT was fancy. Now this. This is revolutionary.
It's gonna be massive once we can combine these, either a next gen chatGPT helping to create a next AlphaFold or direct chat to Protein 😂
Yup. A guy that's all talk but this is all bites
@@DreckbobBratpfanne
"It's gonna be massive once we can combine these"
Such AI -> AI bridges are already possible, and fine so long as you aren't bothered about communication latency vs a singukar multi modal AI.
Tesla FSD was actually doing exactly that up to v11 I think, changing to a sort of multi modal approach for v12.
Well its takes 12 to 15 years become undisputable like the journey of iPhone 1 to iPhone 15 .
They are just started there main objective is to make AGI if agi come it revolutionise the humanity .
It's not. Just a few % over last technique. The guy is presenting it as if it's a second coming of JC. Probably because he partnered with Google on this. Google has sunk Billions into Deep Mind and the shareholders start to ask questions. They are trying to make their investment look good.
Bet AplhaFold 6 will be folding reality itself 😎
not if it keeps being closed-source with carefully curated examples
It will fold my mind into smithereens.
You are AlphaCreate 6 duhh this is what the Egyptians knew how to craft reality
Alphafold 6? More like Betafold 2
@@thegreenxeno9430 Sigmafold Ohio Rizz edition
If a protein can be manufactured to repair human dna, or to recover damaged telomeres, that would probably one of the most impactful biomedical results of all time. To help the elderly regain their strength to live healthier and longer lives by reducing cellular damage and cancer risks would be profound.
I recently lost my grandfather because of age related weakening and loss of autonomy. If something like an enzyme injection could have kept him more autonomous by keeping his fatiguing body healthier, he might even have been alive today.
I lost all my other grandparents to cancer, so if dna repair could help inhibit cancer development from mutation, it would be amazing to see no one ever have to go through what I have gone through again.
Death is inevitable and so is the timing of it. Will take u time to understand..
any sources?@@js_es209
@js_es209 Death may just become a probability that can be mostly mitigate. One day you'll understand.
Our cells already contain proteins that repair damaged DNA. The reason we're even dealing with cancer nowadays is because we live long enough for one to eventually develop in our body, and our own repair systems can't keep up with the rising amount of damage we are now sustaining: carcinogens in the air and in our food, irregular lifestyles, and overexposure to substances and radiations that humanity had otherwise not have access to prior to technological advancement. Without those three conditions, our body's own proteins is probably more than good enough to protect us from cancer, although growing older still means increasing likelihood of developing cancer (because that's just the inevitably of aging).
@@js_es209 not really. There are ways, at least in theory, to become what they call biologically immortal. So, while your assertion may still be true on this day and age, maybe in the future it won't. Ok, probably real eternal life won't be achieved or even desired, but, periods of time which we consider to be long enough might be in the future.
i'm pretty sure they're participating in CASP16 because of this. My lab is participating too. We just agreed that they've already won
Everyone is talking about LLMs, But this is really where impact to the future is being made!
This is made by an LLMs you know that right "Alphofold AI"
LLM*
@@tingtonggamer4901no, I was correct
@@tingtonggamer4901 Oh really? I haven't read the paper. Thanks for pointing it out, I'll check it out
LLMs are at the root of all these developments. Their emergence is an epochal event
I get shivers every time i work with alphafold! to think that it is free. A true testement to the Greatness of human civilisation!
Hey bud! While watching the video I had a question pop up, and seeing that you work in the field maybe you know the answer:
From what I could understand, Alphafold is able to take "letters" as input (aminoacids or something like that I believe, but correct me if I'm wrong), and outputs the 3d shape of them right?
If so, how does that helps with development of things like, the plastic eating enzyme, and other things? Wouldn't you already need to know which letters to use beforehand?
How does knowing the shape of everything affects the development?
Pardon me if I'm saying nonsense. I'm an automation engineer and know almost nothing about biology.
@@lucasreis6251you look slightly autistic
@@lucasreis6251 answer of ChatGPT:
Yes, you understood correctly. AlphaFold takes a sequence of amino acids (these are the "letters" in proteins) as input and predicts their three-dimensional structure. This can help in the development of various biological processes, such as creating a plastic-eating enzyme or other enzymes. Knowing the three-dimensional structure of a protein can help scientists understand how it interacts with other molecules and what changes in its structure could improve its functionality. Thus, even if we know the amino acid sequence beforehand, predicting the three-dimensional structure aids in understanding its function and designing improved versions of the protein.
@@lucasreis6251 So yes you are abselutly correct, you would need to know the amino acids beforehand.
That is luckily a pretty standard thing to get to know. You can do a buch of differnet test (like mass spec) to figure out what amino acids and in which order they are placed.
The almost impossible part to figure out is how the protein folds. It has been a core theory that the the chemistry of the aminoacid chain is what makes proteins fold in specific ways and hold their shape and activity.
But breaching the gap from sequence to folding is a huge task that until alphafold many times took years of research to figure out. What most people did to get as accurate readings as alpha fold was to do crystalografi. That is a very complicated task that needs pure crystals of your specific target protein, which was almost more art than science to make work honestly.
Alpha fold skips this years of wait and hard labor, letting us play with how mutations affect folding in a timeframe of hours. It is hard to overstate the impact of this ability in research.
Hope this answered your question ^-^
edit: realized i didn't answer your question about how protein shape affects development.
All proteins have basically the same amino acids in them. The amino acids are actually not what makes proteins able to interact in a biologically active manner. It is the shape of the protein that does. So to know how a protein interacts chemically you need to know how it folds, and not what amino-acids it has.
@@lucasreis6251 As a biochemist I can answer this. These "letters" are just a human code for amino acids, amino acids are molecules that form polymers (polymers are long-chain molecules that consist of a certain number of repeating connected units). In the case of amino acids, almost all organisms have 20 different of them, using these 20 every protein in your body is created. Proteins can do things such as move your body (muscles), but basically everything else in your cells is done by proteins. Signal transduction in neurons, breaking down nutrients and synthesizing new structures, transport of molecules around your cells, the immune system is also dependent on a lot of proteins (antibodies for example are proteins).
Now, a type of proteins are enzymes, these are nature's catalysts, they can speed up reactions drastically (up to *10^9 !!!). For example we have enzymes that break down sugars into food. It gets interesting when you study bacteria, fungi, plants... Often times they have very specialized enzymes, for example some that can break down polymers. Plastics are polymers as well with often very similar chemical bonds to molecules that bacterial enzymes would break down. If we can mutate/adjust these enzymes to be more efficient at breaking down plastic, they could be a very useful catalyst in such a reaction. This is just one potential use, the possibilities are endless. We can have enzymes that produce lab-grown meat, help with electricity production...
It's very easy to get the sequence of a protein (the amino acids it's comprised of), but how these proteins look structurally (3D) is very hard to find out by traditional methods. Using AI trained on existing 3D models, it can find patterns, for example a code of a certain 10 aminoacids would always fold into a certain structure. This is how predictions are made.
So, now imagine you discovered a new enzyme from some bacteria that can do X, you get its sequence and instead of spending years and thousands of dollars in finding its structure in the lab, you can just plug the sequence into alphafold and get very likely the same result. Based on this then you can find out more about the protein's function, the mechanism of function and the sequence to structure relationship.
I hope it was understandable what I wrote.
Oh I'm holding onto my papers now
Seeing AlphaFold 3 design ligands to help the brain and spinal cord regenerate would be cool, as myelin (and a few other tricks) inhibit neural regeneration
Another interesting use case: exploring SIRT6 variations, its impact on aging, and finding ways to enhance its functionality.
it WILL HAPPEN.
Finding effective remyelination therapies to help people with MS like my daughter.
Are you talking about Lizard man
If that as a medicine can be programmed into a fruit or vegetable or maybe a group of fruit and vegetables eaten together that can be grown it would really be amazing. Also changing the snakes DNA so it can have hands and legs and fruit from a tree that can help women reduce the pain at child birth and robots that can do the hard labour in the sun whose hands cannot be pricked by thorns.
You made me love papers and start reading it. It means a lot to me and thank you for the excellent work as always!
This really made my day. Thank you so much! 🙏
Same for me.
I can imagine a system that can sequence your personal genome and through tons of training be able to discern how exactly you’ll react to certain drugs and what dosage you need. It’s crazy to look back at how far Medicine has come in the last 20 years, it’s impossible to even begin to image the capabilities in another 20 years time.
All advancements start somewhere, and releasing a paper is usually always the first step
That's is a very cool concept 🎉🎉🎉
You just re-invented the field of pharmacogenomics, congrats.
I can literally go do said test right now. It's just currently in its baby stages. I got offered to do said test for 500€ by my psychiatrist, with said disclaimer. The tech will only keep getting better though and once your genome is sequenced, they can just update the treatment with any new way to analyse it.
Do you have any need in mind ?
im so glad that i was born at JUST the right time to enter college for biotech in the infancy of all these new programs. cant wait to actually work with them later in life
Yeah AI will revolutionize Biotechnology forever.
You’re our future and I wish you luck.
I recommend working with them now already!;)
Hary! AI will work alone when you finish the university! SUPERINTILIGANCE
And the Nobel prize goes to Alphafold!
- in what?
- yes
Amazing work again from DeepMind!
As a protein researcher, I'd love to see custom enzymes designed to bind PFAS, or the 'forever' chemicals that interrupt biological processes. Designing an active site to break them down chemically would be next level, but difficult due to the chemistry involved. However, there are other pesky environmental toxics listed as the Stockholm Convention Persistent Organic Pollutants (POPs), that may be more attainable. AI to design enzymes to breakdown environmental toxic chemicals? Sign me up! I'm in.
I wanna dump truckloads of this on old landfills, come back in a few years and maybe it'll all be free compost...
@@JohnVance I guess that it won't work like this before some time.
I fold my papers... Too good...
... and actually Imagine where we'll be just two more folds down the line!
41 more folds to reach the moon!
I thought it’s impossible to fold paper more than 5 or 6 times?
Sigh, it's amazing how everything is about to 'change everything' and yet nothing ever seems to fundamentally change.
If you had a president take a space race approach to this technology you'd see a lot change. Something like "let's fundamentally eliminate biological failure as a cause of death within 10 years", and throw space race money at it, and you'd probably be able to pull it off. Would require a lot of planning though. Problem is that much more is *possible* than anyone has the authority or administrative capacity to implement, when it comes to all that sci fi stuff. Would require a society making a decision, which is a bigger barrier than the technology itself at this point.
Our politicians do not work for the people. They work for corporations. That's why they're trying to be careful not to eliminate just worker jobs but also not make their industry or business obsolete in the future. They are going slow not only to be safe but to line their pockets with profit
I mean, we said the same thing about the internet and the smartphone. Sure we have hype about eventual flops like NFTs, but you can't say something like email hasn't fundamentally changed the world in 30 years. And even stuff like enzymes are all in your detergents and your cosmetics. It doesn't change until it does, all at once.
@@adissentingopinion848 Sure, but one just tires of the constant rhetoric that everything is always being revolutionised while day to day life is more of a struggle than ever. I think we just need to tone down the rhetoric a little.
It is also a game of patience. Lots of these are like designer custom made parts. You'd need to market it to scale it up enough for people to afford it, and that requires large initial funding... Which requires a Monetary incentive to do it.
Basically, unless the enzymes break plastic into gold or companies/people(worst case) are taxed for plastic waste accumulated, there is no incentive to break down plastic until it is a dire threat
Wow, DeepMind almost listened! I've told them since releasing AlphaFold that what is needed is a neural net that predicts the structure of a hypothetical ligand for some selected area of the protein. Meaning, you give it sequence A and it calculates structure B. You would then highlight an area on B that you want to bind to (like the reactive site of an enzyme) and it will then generate ligands that would fold in such a way that there would be geometric and chemical affinitiy with the highligted area.
This isn't exactly as good as that, but atleast we are getting the joint structures, which is an improvement.
Anyone with connections to DeepMind, please share my feedback with them, seems they have not seen the comments/emails during these five years.
This is huge. There are so many illnesses that we know what the mechanism is right down to the proteins, but we just don't have any drugs for that are effective other than for treating the symptoms. This could also allow us to precisely target treatments to the illness much easier.
Curing people doesn't make money. Creating new illnesses makes money..Guess which one is coming your way..
Absolutely love these longer videos. Can’t get enough of your enthusiasm and the paper news
can it help to make cat girls
The highest of all high technologies; the final technology man will ever invent (because he can't be bothered with anything else after that).
It can make all the proteins but i dont think it can use them to build your cat girl
I hope longevity medications coming soon for mum and dad :)
100% agree, I think research on interventions to the aging process needs much more attention and funding.
Same, my dad is getting super old!
Pretty sure that would come with a rather large can of worms.
Nope.
They will start on other animals first - likely significant life extension for domestic pets.
@@mnomadvfx Nope- they will take human volunteers on their death bed.
Holy paper! This is amazing! I imagine how this would work when newer advancements in agents and planning, as well as architecture advancements (such as Jamba proved) will affect this! Imagine how lab work will change with these new tech!
Ligands for breaking cellulose out of wood for paper manufacturing that reduce smell and waste discharge.
What a time to be alive! 🎉
Just company bullshit. Protein folding accuracy needs much more than only this program. They just sell nonsense!
Very excited, I am working on a project where i used AF2 to predict better binding antibodies mixed with some reinforcement learning. I emailed everyone I know in university about the AlphaFold3, so excited.
Hey bud! While watching the video I had a question pop up, and seeing that you work in the field maybe you know the answer:
From what I could understand, Alphafold is able to take "letters" as input (aminoacids or something like that I believe, but correct me if I'm wrong), and outputs the 3d shape of them right?
If so, how does that helps with development of things like, the plastic eating enzyme, and other things? Wouldn't you already need to know which letters to use beforehand?
How does knowing the shape of everything affects the development?
Pardon me if I'm saying nonsense. I'm an automation engineer and know almost nothing about biology.
@@lucasreis6251you are right，but same ‘letters’ can consist different shape and this shape detect different fraction.
@@lucasreis6251i have a rough idea but lets wait for him
His must be better
This is incredible! I really hope all undergrad colleges could incorporate Alphafold-3 in their research so that the students of this generation can take advantage of this revolutionary technique!
I can't wait for the applications of these models to never make it to general use because of politics, or have them completely monopolized by big companies.
I love how in a couple of years, all of this channel's content will definitely be done by AI.
Even his voice sounds already auto generated already.
What a time to be "alive" !
How dare you! Only a human is capable of sounding this stilted and unnatural! XD
I want Dr Károly's voice in GPT-4o.
I want Dr Károly's voice in GPT-4o.
I have been using AlphaFold 2 for my thesis and it helped me so much understanding the protein I was researching. I am so hyped for this ❤
I've already told you,
but I'll tell you again:
you are doing a lot to make tomorrow a better world,
an enzyme to recycle plastic.
The world lacks people like you.
Got my hello world on the AlphaFold 3 server!! Thank you for this video Two Minute Papers! WHAT A TIME TO BE ALIVE!
Will these systems be leveraged as commons for the better of mankind, or foreclosed by a bunch of heirs atop predatory funds? I am positively happy that such progress is made, and ever so pessimistic about who will reap the benefits.
Folding on to my papers!
Honestly I would like to see some annotations about the function of the differents parts of each protein structure. That would be so cool!
Have been following Deepmind since Alpha Go days...and am really inspired by their AI for Good approach. Thanks for sharing it. Do consider doing a AMA online sometime for all of us. Cheers
had to mute the voice and turn on cc but in the end it didn't matter cause i really didn't see the big deal . guess i'm not well informed about this whole protein folding science.
I think it is merely bs. Protein folding by computer is not precise enough - a lot of interactions (h-h bridges) are just crudely approximated and you still would need a super computer as a neural network even bigger as every element of the universe to make it fold like in real time. The most precise models are when you combine protein x-ray crystallography with protein folding programs.
what a time to be alive! thank you so much!
"How could it possibly be better?!" As a protein scientist I can safely claim that AlphaFold2 was useless to me. Very happy to see the research charging forward in this field
This.
You should know (as a protein scientist) that those computer simulations are still not even close to predict accurate folding of a protein!
I love our human ingenuity! ♥️
Dude! I'm actually flipping out at this bar chart!
I LITERALLY Made a 5-page paper.. on mealworms specifically superworms that broke down plastics and got calories from them and were able to reproduce from the plastic diet thanks to their enzymes. Finally, this is getting attention, making those enzymes into like an artificial stomach to at least turn plastics into Glycol is better than nothing!
This is one of the coolest things I've heard of in my life.
HOLY mother of Fpapers!
Best part of this was them supplying all the pseudo code and training datasets. Hopefully Rosetta Commons will drop an open source version soon
Definitely looking forward for other molecules, along with their interactions (the dynamism you referred to) is imo the most exciting possibility. The fact that this may be doable in the next few years, given these truly amazing developments, is just totally mindblowing.
What a protein time to be folded alive! 🎉
this is crazy exciting for the next update damn
I'd like to see an enzyme that could break down interstitial amyloid plaques to prevent or slow the progress of Alzheimer's.
Amyloid plaques appear to be a symptom of AD, not a cause. They seem to be a kind of defensive or homeostatic mechanism in response to insufficient nutrition in brain cells, with the function of downsizing brain volume to keep more important areas of the brain well-supplied. Treatments which reduce or prevent amyloid plaques have shown to be ineffective, and in fact counterproductive, in halting or reversing the progression of the disease. Tau protein tangles and buildup of protein in cerebrospinal fluid during the prodrome of the disease seem to be more material to the pathogenesis.
@@4grammaton Interesting. I read (5+ years ago now) that the plaques naturally build up and eventually encroach on synapses. I will refresh my knowledge.
@@SteveRowe Please do, and feel free to inform me if what I said is inaccurate. I also remember reading that plaques are found even in the brains of young children.
all of life's molecules mapped
I have been keeping up with developments in AI for the last couple of years, and have lost count of the new developments that will 'change everything'.
I look out the window and nothing's changed, I go to my place of work, nothing has changed, I watch TV and sports, same thing, no change. Nothing has changed in 2 years apart from some online AI programs that'll give you pictures, videos, music, essays from a prompt, it's fine and all, but it hasn't 'changed everything'
It's like crying wolf every 5 minutes, the 'changes everything' hype just becomes white noise.
The only thing that's really changing is the increasing level of fakeness.
It feels like where in the bubble phase of this technology where people see potential everywhere but there is no actual use, so there’s a race to find it. It reminds a lot of the dotnet bubble. People claimed the Internet would change everything for years and only after the bubble popped and a small number of products survived did change start to happen. Well and now its hard to find a place in everyday life where the internet didn’t change something.
Having choose to Fold@home in the early 00s rather than mine bitcoin, I am glad to see this field has grown so much.
This kind of progress may be more important than all those other AIs. Medicine > Other stuff
In 2004 I was ingressing University to course Biological Sciences. If you asked anyone there how much time they'd think it would take for mankind to see an applicable tool with the capabilities and accuracy of Alphafold you wouldn't hear "20 years" even from the most optimistic.
What a time to be alive!
Great video as always! I have a question. Is there a platform I can "subscribe" to read new papers in my fields of interest? AI, Psychology, etc. What are some good platforms I can subscribe to? (I am not a university student, so I don't have access to the main libraries of papers without having to pay for them 😢)
arxiv
"Letters go in and a 3-D structure comes out. You can't explain that."
I was in my final year or biochemistry in 2018 and we were discussing the protein folding problem where the lecturer said estimates for solving it are around 25 years aways. Next year alphafold went mainstream.
Meanwhile Apple has made a squeezable pencil
😂😂😂😂
How many times has something changed everything without anything actually changing?
What a time to fold proteins!
looks like the next Nobel prize awardee!!
WOW this is amazing. Wonder if we can build a text to protein transformer with this technology to find new proteins based on textual descriptions of use cases and associated receptors...
Fantastic paper, thank you
Amazing!
Can someone shed light on why these ml models work better than the ones more rooted in physics? To me it seems like this should be a first principles based problem considering the causal non-entropic physicality of it. For example, we similarly have calculators to do math since the rigid rules are part of the ground truth (E.g. transformer based LLM models predicting the next token are worse at adding numbers than a calculator).
I ain't a guy that does much personal work with AI, but from what I gather it's mainly because this AI model can "intuit" to approximations and skip over many steps, then go back and verify it, and adjust its answer until it's as close as it can get. rather than having to work through the calculations done for a physics based interaction with many points of failure that can cause a cascade of inaccuracies to develop due to small errors and the like.
Again, take it with a grain of salt, that's just my best guess
I'm flattered on behalf of humanity that you decided to interact with humans before consulting with an AI,
My human reply would be that I guess the physics based algorithms are based on physics as we understand them and are more limited as they're only as good as we understand physics. A full general AI can take inspiration from any element in the world that would boost the chance of success. So less precise because it's not rooted in physics yet more precise because of the insane amount of datapoints as inspiration.
Chatgpt 3.5
Machine learning models like AlphaFold 3 outperform physics-based approaches in protein folding due to their ability to learn complex patterns from vast amounts of data. While physics-based methods rely on rigid rules and principles, they often struggle with the inherent complexity of biological systems. ML models, on the other hand, can capture subtle relationships and nuances in the data, leading to more accurate predictions. However, it's essential to note that both approaches have their strengths and weaknesses, and a hybrid approach combining the best of both worlds may yield even better results in the future.
PS, this is just me trying to come up with an answer to your question because it was a good question and I'm curious.
I'm definitely no expert but from my engineering experience when it comes to simulating complex processes with algorithms errors tend to stack quickly and so your result loses reliability the more iterations are ran. Artificial intelligence systems have the benefit of "knowing" roughly what the output result should be expected as, whilst an algorithm has to be tuned either by the operator or a separate algorithmic process (With much the same issues as before). The intelligence model is probably never going to be exactly accurate as it doesn't solve the problem as a series of fundamental physical rules of nature but instead through user defined rules. The physics model will probably never be exactly accurate because noise is inherent in the system. A weird analogy I think of is if the two systems are both set out to solve a jigsaw puzzle the intelligence algorithm takes premade data (That may not be neccesarily accurate) in the form of puzzle pieces and tries to make the picture as you and I would, but will always lose data in the gaps and overall accuracy. On the other hand the physics algorithm attempts to cut out its own pieces which can sometimes be effective but compounds errors as it goes. As I say tho, I am no expert, just having some fun with the ideas
We simply do no have the compute, because these calculations scale unfavorable. These new models seem to somehow compress the data. Its like the game of life, simple rules can create complexity
From what I understand it isn’t a problem of accuracy but of computing power. If an AI gets decent at learning the higher order ‘rules’ which govern protein folding it can look at a sequence of amino acids and give an educated guess on the shape it would likely take under certain conditions without having to calculate millions interactions between hundreds of thousands of physics objects.
It makes it viable for a researcher to identify promising novel drug candidates within a search field of millions of possible amino acid sequences without needing to invest in thousands of years of supercomputing time or the obscene amount of lab time and resources that would be required in order to to test each novel substance in vitro.
The very fact that AlphaFold even works is huge - it means that behind the insanely complex Van-der-Waals physics of millions atoms interacting, there is some really good analytical approximation hidden with a tiny computational cost. If machine learning could uncover such a system, there is a good chance that we'll eventually discover it analytically, and this will be the real game changer.
For the non-biologists here (myself included), how close does this get us to designing more specifically targeted drugs without undesirable side-effects?
A friend of mine is curious to know, too.
In a nutshell: To predict correct protein folding is absolutely insane. In reality: You need actually to concentrate the real protein and use x-ray crystallography and a simulation like this to get a quite precise glimpse how it fold. I think this advertising for this program just ignores that. A solely simulation can’t predict folding of a protein (not even close). Peptides (very short proteins) are eventually possible so take this advertising with a grain of salt. Yes it will fold your proteins and give you some insights but no real scientist would put their hand into fire that he/she trusts a program like this.
1:43
What you just said guaranteed the perenity of plastic's use in industries. This may even help recycle Reticulated plastics, enabling recycling of composites!
Although I'm tremendously excited about this advancement, as a biotechnologist myself, it ought to have been mentioned that right now the list of available ligands that are compatible with AF3 is actually very small and so if you're trying to model interactions between proteins and any molecules that aren't incredibly mainstream you're out of luck right now. Certainly no scope for users outside of DeepMind and Isomorphic to use it for ligand design at the moment.
Alpafold: we made something that will change the world
Government: 🔫
Holy Mother of all Papers...
this arrived way earlier than i imagined :0
What a time to be ALIVE!!!!
Absolutely huge!
Just a few more papers down the line and it'll figure out abiogenesis, what a time to be alive!
Amazing! What a time to be alive! 🧬
great progress lets see if it can bring back hairs
Thank you for your work!
I "held on to my papers" and am impressed
These papers give so much optimistic hope for the not so distant future 😁
I'd like to repeat the seminal work of Chothia and Lesk, laying the groundwork for protein structure biophysics with a couple of dozen protein structures in the 1970s, re-applied to the vast universe of new protein structures. This would be a tribute to the late Cyrus Chothia, who saved my PhD (and probably my life).
Que emocionante resultan estos avances! Amazing! Alphafold 3
Thankyou for sharing!
The first question I have about enzymes,
that decompose plastic is.
How do you make sure that the enzymes only decompose the plastic,
Which one do you want to have decomposed?
Especially when they are used in the environment and not just in the laboratory.
But the AI is very Impressive.
Holding my papers !
Demis Hassabis and the AlphaFold team deserve a Noble Prize in medicine for this system!
Drug discovery faces a significant hurdle with target validation. If AlphaFold 3 simplifies this, it could save billions and years of research typically wasted due to inadequate in silico validation. At our lab, we are testing a new quantum computing tool specifically for that purpose. It would be interesting to see how AlphaFold 3 performs on the same tasks.
Antipsychotic medication and receptor ligands would be awesome, finding interactions between medication and receptors, or drugns and receptors(protein structures)😅
As a Beer transport researcher I got excited at the low score of 7:33 no IPA😂😂
Aging gracefully without pain and be fit and young at the same time. Constant improvement in quality of life. (And wars must be banned.)
This seems to be great! WOW!
Perhaps I'm too old school. But I would get really excited if we could learn principles or form methods or theories from these improved results that can improve our understanding. I inherently dont like the idea of trusting complex purely to ai without any understanding of the results
The thing is, we already understand a lot - if not most - of the mechanics at play here. We just haven’t had computationally efficient algorithms to do it.
Okay, obviously I dont know anything about protein folding algorithms, so to simplify and generalize my comment - i wish ai would make us smarter, enhance us, make us able to produce whatever wonderful results
Thanks for the info 👍🙂
I would love to see it use to create a nootropic, some thing like the NZT-48 of limitless