Googles ALPHAFOLD-3 Just Changed EVERYTHING! (AlphaFold 3 Explained)
Google’s AlphaFold-3 has just changed the game in the field of AI with its remarkable ability to predict the structure and interactions of all of life’s molecules. In a groundbreaking announcement, Google DeepMind and Isomorphic Labs introduced AlphaFold 3 as a new AI model that can accurately predict the structures of proteins, DNA, RNA, ligands, and more, shedding light on how these molecules interact with each other. This breakthrough technology is set to revolutionize our understanding of the biological world and accelerate drug discovery processes.
AlphaFold 3’s next-generation architecture and training cover all of life’s molecules, allowing it to generate accurate 3D structures of biomolecules within hours or days, a task that would typically take months or even years using experimental methods. By accurately predicting how molecules interact with each other, AlphaFold 3 is paving the way for faster and more efficient drug discovery, offering new possibilities for treating diseases like cancer and COVID-19.
Isomorphic Labs is leveraging AlphaFold 3 to accelerate drug design and create novel treatment modalities, such as antibodies and therapeutic proteins, based on the AI’s structural predictions. The AlphaFold server, which allows scientists to generate models of proteins, DNA, RNA, and other molecules for free, is empowering researchers to explore new ideas and hypotheses in the lab without wasting time on trial and error. With AlphaFold 3, the future of science has just gotten a whole lot brighter.
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Video Transcript
so Google deepmind and isomorphic Labs have just surprised the industry by releasing Alpha fold 3 and announcing how good it truly is so it says Alpha fold 3 predicts the structure and interactions of all of life’s molecules you can see here it states introducing Alpha 3 a new AI model developed by Google Deep Mind and isomorphic Labs by accurately predicting the structure of proteins DNA RNA ligans and more and how they interact we hope it will transform our understanding of the biological world and Drug Discovery so you have to think about it like this in every cell of every living thing plant animals even us there are literally billions of these microscopic machines and these machines are made up of proteins DNA and other funky molecules and the thing is is that none of these pieces work alone they’re all kind of interacting combining in millions of ways and only by seeing that interaction can we actually understand understand how life works and this is where Alpha 3 comes in they literally just published a pcture in nature magazine which we’ll get into later in which they talk about this amazing new AI model and this model can literally predict the structure of life’s very molecules and even how they interact with crazy good accuracy and we’re actually talking a significant leap on what we could do before and the crazy thing is is that this is probably about to show us how all those crazy crazy machines fit together why they behave the way they do and this is the key to understanding everything from diseases to how plants grow and how to fix problems or build new awesome stuff and the details of this are pretty pretty crazy and it’s pretty incredible that they’ve managed to build upon the success of alpha Fall 2 which was the one that changed the game in understanding proteins and researchers everywhere actually do use it think of malaria vaccines cancer research the entire ire whole deal and Alpha for’s already been such a GameChanger it’s even one major science Awards and Alpha for 3 it actually goes Way Beyond just proteins to all sorts of biomolecules think eco-friendly materials stronger crops supercharged medicine this is pretty much next level science with the power to change the world so how does this actually work so given a list of input molecules Alpha fault 3 generates their joint 3D structure revealing how they all fit together it models large biomolecules such as proteins DNA and RNA as well as small molecules also known as ligans a category encompassing many different drugs and they can model chemical modifications to these molecules which control the healthy functioning of cells that when disrupted can lead to the disease we also see that Alpha folds 3’s capabilities come from its next Generation architecture and training that now covers all of life’s molecules at the core of the model is an improved version of the Evo former module which is essentially a module that kind of learns the grammar of protein folding by studying evolutionary examples and then uses that knowledge to predict the 3D structure of new amino acid sequences much like how we can kind of predict the meaning of a new sentence after learning the grammar of of a language and it’s a deep learning architecture that underpinned Alpha folds 2’s incredible performance and after processing the input Alpha for 3 assembles its predictions using a diffusion Network akin to those found in AI image generators and the diffusion process starts with a cloud of atoms and over many steps converges on its final most accurate molecular structure now here’s where we have one of the predictions so this in well in this case what we do have here is we have the ground truth shown in Gray and then we have the real one shown in the actual colors so in this example what we do have here is we have us looking at the spike of a protein of a common cold virus the spike protein is a part of the virus that helps it infect our cells and the AI model actually accurately predicted how this Spike protein interacts with antibodies which are the immune systems defense proteins that attach the virus and neutralize it and of course simple sugars in this prediction that you’re currently seeing on screen the spike protein is in blue the antibodies which try to stop the virus are shown in turquoise so the simple sugars are also shown in yellow and these predictions essentially closely match what scientists have observed in real life experiments which are shown in Gray by using animations of this interaction scientists can then see exactly how the virus actually interacts with antibodies and sugars and this information is crucial because understanding how these immune system processes helps us figure out how to fight different viruses including covid-19 leading to the potential of better treatments and Alpha fold 3 saves so much time by providing accurate predictions that would otherwise require lengthy and expensive laboratory equipments and it does this because determining the 3D structure of proteins using experimental methods like x-ray crystallography or cryo electron microscopy can take months or even years and alphaa 3 can predict these structures in literally hours or days and with predicted structures available scientists can then focus on the most promising drug Target or biological questions without spending time exploring dead ends and this allows researchers to test hypothesis so there’s hypothesis generation where it can generate new hypotheses about how biological molecules function or interact and researchers can then test these hypotheses directly reducing the need for broad exploratory studies now there was also another example here in which we can see Tim 3 This Is A protein that researchers are studying because it might be useful SL a useful Target for cancer treatment and scientists found a way to create small molecules that could stick to this protein and potentially block the harmful effects now before this study there weren’t any clear images showing how these small drug-like molecules would actually fit into the Tim 3’s structure and without this information designing effective drugs was pretty challenging so essentially Alpha fold 3 comes in scientists use Alpha fold 3 to predict what Tim 3 would look like when these small molecules bind to it and they only provided the AI with the protein sequence which is essentially the recipe and a simple description of the drug like molecules so that’s where we get to the outcome so Alpha fold 3 actually predicted how these molecules would fit together perfectly into the pocket of the Tim 3 protein aligning almost exactly with the structures that scientists discovered through experiments it also showed that without these drug molecules present the pocket actually looked different proving that Alpha fold 3 can actually recognize changes in protein shapes when other molecules are around and this essentially means that Alpha fold 3 can predict how drug molecules will interact with proteins more accurately than ever before and this is going to lead to fast and more efficient drug Discovery helping scientists developed better treatments for cancer and other diseases and of course it makes sense to talk about isomorphic Labs so one of the things that they talk about leading this drug drug Discovery at isomorphic Labs is that alphafold 3 is 50% more accurate than the best traditional methods on the pose Busters Benchmark without needing the input of any structural information making alphaa 3 the first AI system to surpass physics based tools for biomolecular structure prediction and isomorphic Labs is using alphafold 3 to accelerate and improve the success of drug design by helping understand how to approach new disease targets and developing novel ways to pursue existing ones that were previously Out Of Reach they also talk about how we can now create and test hypotheses at the atomic level and produce highly accurate structure predictions within seconds standing in STK contrast to the months or even years require to experimentally determine answers to similar questions now they also talk about how they’re using this they state that already we are using alphafold 3 dayto day our scientists have seen that designing small molecules against alphafold 3’s structural predictions helps create designs that bind effectively to a Target protein the improved structural accuracy of protein to protein interfaces with Alpha fall 3 opens up the possibility of Designing new treatment modalities such as antibodies or other therapeutic proteins and a richer understanding of a novel Target can be achieved by looking at the structure of Targets in their full biological context in complex with other protein binding Partners DNA RNA and ligand co-actors and of course there was a paper that was released with the alpha fold 3 release however this is currently an accelerated article preview an AAP which is a version of a scientific article that’s published online before it appears in a traditional print journal and it basically just means that it’s just designed to get important research findings out to scientists and the public as quickly as possible and they kind of skip some of the editing and formatting that can actually slow down a traditional Journal publication and that means that there is like a watermark on each page to remind you that they aren’t final the final polished version now here’s where we actually talk about the main thing which is of course the alpha fold server so Google actually launched this tool that actually helps you do this stuff so scientists can actually use this for free there’s no fancy subscription needed and basically with a few clicks any battes can use Alpha fall 3 to make models of proteins DNA RNA and other important molecules and this is pretty huge because the alphaa server lets scientists quickly come up with new ideas to test out in the lab and this cuts out the time on wasting guesswork so just just picture your science projects going way faster and remember this used to take you a huge amount of time and now all of that is being saved so this is the quick trailer I’ll leave you guys with this and if you need any of the links there will be either at a top comment or a link in the description [Music] [Music] [Music] [Music]
Video “Googles ALPHAFOLD-3 Just Changed EVERYTHING! (AlphaFold 3 Explained)” was uploaded on 05/08/2024 to Youtube Channel TheAIGRID