Life’s Molecular Blueprint: AlphaFold 3 Changes Our Biological Understanding
A simplified and condensed review of the free AlphaFold Protein Structure Database, drawing on authoritative sources and analyzing a recent landmark paper published in Nature.
Last month, in May 2024, Nature, one of the most prestigious scientific journals, published a remarkable paper titled “Accurate structure prediction of biomolecular interactions with AlphaFold 3,” authored by 48 esteemed scientists citing 73 prior scientific citations. Having had the privilege to read the early version, I now eagerly share its transformative potential with my clients, students, and protégés.
When I surveyed some of my loyal Health and Publication subscribers on Medium and Substack, they asked about the most pivotal scientific advancements that could change our lives. Without hesitation, I point to AlphaFold 3 as that game-changer. I will cover others in another story.
In a conversation with one of the peer reviewers, I learned that Nature chose to publish this article because of AlphaFold 3’s revolutionary capability to predict 3D protein structures with great accuracy. This breakthrough is set to revolutionize drug discovery, disease research, and our understanding of complex biological and evolutionary processes.
The tool democratizes access to cutting-edge predictions through the AlphaFold Protein Structure Database which I will introduce below, accelerating global research and paving the way for scientific discoveries and technological innovations.
Its interdisciplinary applications span materials science, renewable energy, and environmental science, showing its extensive impact.
Nature’s rigorous peer-review process ensures the integrity and significance of this work, while the publication brings much-needed attention to AlphaFold 3’s potential to tackle global health and food security challenges.
You can access this valuable paper through this public link.
An Overview of AlphaFold 3
Imagine peering into the intricate machinery of life, where billions of molecular machines whir and interact within every cell of our bodies. This imagination might take you to an altered state of mind as it does to me.
AlphaFold 3, an advanced AI model, is providing scientists with a clear view of the intricate interactions among proteins, DNA, RNA, and other essential molecules.
This is beyond a scientific curiosity now. I see it as a game-changer in the science world. AlphaFold 3’s ability to predict these interactions with remarkable accuracy can transform how we understand biological processes, from the mechanisms of disease to the development of new drugs.
Remarkably, AlphaFold 3 enhances existing prediction methods by at least 50% and, in some cases, doubles their accuracy. This sophisticated tool far surpasses generative AI models that have already captivated the public’s imagination, sometimes leading to misuse and abuse.
Building on the success of AlphaFold 2, which revolutionized protein structure prediction using computational methods, AlphaFold 3 expands its capabilities beyond proteins to cover a broader spectrum of biomolecules, including DNA, RNA, and ligands. This expansion offers valuable insights into the complex molecular interactions that underpin life’s processes.
This breakthrough is already being used by Isomorphic Labs to accelerate drug discovery and development, offering hope for new treatments for various diseases.
The best part for us, in my view, is that most of AlphaFold 3’s capabilities are freely accessible to scientists worldwide through the user-friendly AlphaFold Server.
This means researchers, regardless of their resources or expertise, can now explore the intricate world of molecular interactions and unlock new avenues for research and innovation.
From designing bio-renewable materials and resilient crops to unraveling the mysteries of genomics, AlphaFold 3 is poised to revolutionize numerous fields.
Its ability to model complex molecular structures and interactions in stunning detail is opening up a new era of scientific discovery.
But, of course, with great power comes great responsibility.
The developers of AlphaFold 3 prioritize responsible use, collaborating closely with the research community to mitigate potential risks and promote ethical applications. Ethics play a crucial role in advancing groundbreaking science and technology.
Without ethical control, the world of science and technology would gallop like untamed horses in the civilized world, charging ahead without regard for consequences or direction.
The developers’ goal is to democratize access to this transformative technology, empowering scientists across the globe to tackle some of humanity’s most pressing challenges.
The discovery of AlphaFold 3 marks a monumental leap forward in our understanding of the biological world. As we study the complex interactions of molecules within our cells, we uncover insights that will shape the future of medicine, agriculture, and many other fields. The potential for positive impact is truly remarkable.
An Example of Practical Use
Recently, my mentor, Dr. Yildiz, authored an article on Medium titled The Nuances of Phytic Acid (Phytate) for Health and Disease on my publication. When discussing the reason and impact of the story, knowing my background in protein modeling, Dr. Yildiz asked if I could provide him with models of several phytate-related organisms for his clients’ science project. I showed my willingness to help using AlphaFold 3, I generated and delivered three detailed AlphaFold structure predictions.
For instance, the database indicated that the protein 3-phytase, encoded by the gene phy, originates from Bacillus subtilis (strain 168), a bacterium.
According to its UniProt entry P42094, this protein has no experimental structures available in the Protein Data Bank (PDB). Additionally, its precise biological function has not been documented, as indicated on its UniProt page.
Here is a sample model view that I provided to Dr Yildiz for his project:
Here are the 252 predicted structures in the AlphaFold Protein Structure Database clustered using MMseq2 and Foldseek. This data is provided by the AFDB Clusters.
You may wonder how I found this information and how long it took me.
I went to the AlphaFold Protein Structure Database, which was developed by Google DeepMind and EMBL-EBI.
Finding the initial information took me just 5 minutes. However, transforming it into a comprehensive and useful report for Dr. Yildiz required around 20 minutes. I used my statistical and qualitative data analysis tools, which I will introduce in an upcoming scientific research tutorial for my readers.
What does my story mean to my health and science readers?
The key message of my story is that AlphaFold 3, a groundbreaking AI model developed by DeepMind, is revolutionizing our understanding of the molecular basis of life and accelerating scientific discovery.
This advanced technology allows scientists to predict the complex interactions between proteins and other biomolecules with unprecedented accuracy, opening up new possibilities for drug design, disease research, and various other applications.
For scientists and clinicians, this means access to a powerful tool that can significantly accelerate their research and potentially lead to new breakthroughs in medicine and other fields.
They can learn more about AlphaFold 3 and its applications through the AlphaFold website and the AlphaFold Protein Structure Database. They can also contribute to its development by using the AlphaFold Server to predict new structures and share their findings with the scientific community.
For the general public, this story highlights AI’s potential to transform our understanding of biology and improve our lives. It emphasizes the importance of continued investment in scientific research and development.
You can learn more about AlphaFold 3 and its implications by following science news and updates from Google DeepMind and exploring educational resources on their website. They support scientific research by advocating for policies promoting innovation and funding scientific endeavors.
Here are the key references to get you started.
If you have a scientific background, you can start reviewing the new paper published in Nature. It also has 73 links to other scientific papers.
Nature paper informs that AlphaFold 3 will be available as a non-commercial usage only server at with restrictions on allowed ligands and covalent modifications. This means, in simpler terms, with limits on which molecules and changes.
Then, you can start the AlphaFold Protein Structure Database:. The publicly accessible database containing millions of protein structure predictions generated by AlphaFold. Visit the database.
If you have science and technology background you can join AlphaFold Server:. The free online platform where researchers can access AlphaFold 3 to predict protein structures. Access the server.
Another useful resource is Isomorphic Labs. The Alphabet company working on applying AI to drug discovery, leveraging AlphaFold 3. Learn more about Isomorphic Labs.
These resources provide in-depth information about AlphaFold 3, its development, applications, and potential impact on various fields. They offer a comprehensive overview of this groundbreaking technology and its significance for scientific research and innovation.
Final Words
In essence, AlphaFold 3 represents a significant step forward in understanding and manipulating life’s fundamental building blocks.
Its potential impact on medicine, biology, biochemistry, agriculture, and several other fields is immense, offering a glimpse into a future where scientific discoveries can lead to breakthrough advancements for humanity.
Like all significant advancements, both AlphaFold and AlphaMissense data (which I’ll explain in another story based on a review from Nature) come with certain caveats and risks. Here is the disclaimer for users.
“The AlphaFold and AlphaMissense Data and other information provided on this site contain predictions with varying levels of confidence, is for theoretical modelling only and caution should be exercised in its use. It is provided ‘as-is’ without any warranty of any kind, whether expressed or implied. For clarity, no warranty is given that use of the information shall not infringe the rights of any third party. The information is not intended to be a substitute for professional medical advice, diagnosis, or treatment, and does not constitute medical or other professional advice. The AlphaFold and AlphaMissense Data have not been validated for, and are not approved for, any clinical use. Use of the AlphaFold Protein Structure Database is subject to EMBL-EBI Terms of Use.”
Thank you for reading. I wish you a healthy and long life. I published it originally on Substack, where non-members of Medium can read it for free.
If you write about health and science, you are welcome to join my publication. Here is the link to the initial submission guidelines. Here is a sample of how I curate stories from Health & Science publication on Medium.com. Top 10 Stories Published on Health & Science Publication for Friends of Medium
Uplifting Update on My New Pub
My new little publication, Health and Science, made a huge impact, and it is growing as fast as its big brother, ILLUMINATION. I wrote my first newsletter yesterday as it got thousands of views in May 2024. You may read the details from my first juicy and uplifting newsletter titled Exciting Updates from the 1st Successful Month of Health and Science Pub on Medium.
Recently, I introduced three writers, contributing to my publication Health and Science. I will introduce more writers soon. In the meantime, let’s support these writers 🙏
Meet Dr Adam Tabriz, MD, on Health & Science Publication of ILLUMINATION
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Mike’s Favorite Stories on ILLUMINATION Publications — #150 💐
About Me
I am a retired scientist in his mid-70s with several grandkids who keep me going and inspire me to write on this platform. As a giveback activity, I volunteered as an editor for Illumination publications, supporting many new writers. I will be happy to read, publish, and promote your stories. You may connect with me on LinkedIn, Twitter, and Quora, where I share stories I read. You may subscribe to my account to get my stories in your inbox when I post.
You wrote this story clearly and with passion, Mike. I am glad you repurposed it on both platforms. It is hard to find scientific stories understandable to the public.
Fantastic article, Mike! The breakthrough capabilities of AlphaFold 3 that you highlight are truly revolutionary. As someone deeply invested in health science, I’m excited about its potential to transform drug discovery and disease research. Thanks for breaking down such a complex topic and sharing its profound implications with us! 🚀🔬