The structure of human interleukin-12 protein bound to its receptor, as predicted by machine-learning software.Credit: Ian Haydon, UW Medicine Institute for Protein Design Software that accurately determines the 3D shape of proteins is set to become widely available to scientists. On 15 July, the London-based company DeepMind released an open-source version of its deep-learning neural network AlphaFold 2 and described its approach in a paper in Nature1. The network dominated a protein-structure prediction competition last year. Meanwhile, an academic team has developed its own protein-prediction tool inspired by AlphaFold 2, which is already gaining popularity with scientists. That system, called RoseTTaFold, performs nearly as well as AlphaFold 2, and is described in a Science paper also published on 15 July2.
They are large complex molecules, made up of chains of amino acids, and what a protein does largely depends on its unique 3D structure. Figuring out what shapes proteins fold into is known as the "protein folding problem", and has stood as a grand challenge in biology for the past 50 years. In a major scientific advance, the latest version of our AI system AlphaFold has been recognised as a solution to this grand challenge by the organisers of the biennial Critical Assessment of protein Structure Prediction (CASP). This breakthrough demonstrates the impact AI can have on scientific discovery and its potential to dramatically accelerate progress in some of the most fundamental fields that explain and shape our world.
"I didn't think we would get to this point in my lifetime." That's how one research leader in structural biology responded to last week's publication of research in which artificial intelligence (AI) was used to predict the structure of more than 20,000 human proteins, as well as that of nearly all the known proteins produced by 20 model organisms such as Escherichia coli, fruit flies and yeast, but also soya bean and Asian rice. That is a combined total of around 365,000 predictions1. The data, publicly accessible for the first time (see https://alphafold.ebi.ac.uk), were released online on 22 July by researchers at DeepMind, a London-based AI company owned by Google's parent company, Alphabet, and the European Bioinformatics Institute, based at the European Molecular Biology Laboratory (EBI-EMBL) near Cambridge, UK. DeepMind's AI predicts structures for a vast trove of proteins The DeepMind team developed a machine-learning tool called AlphaFold.
Kristóf is Founder and CTO at Turbine.AI, and holds a PhD in molecular biology and bioinformatics. To inquire about contributed articles from outside experts, contact email@example.com. Could you predict how an airplane flies only based on an inventory of its parts? This – with proteins – is the essence of the protein folding challenge. Two weeks ago, the organizers of the CASP protein folding challenge just announced that DeepMind's AlphaFold essentially solved the challenge – its prediction score was just below experimental error.
Last month, DeepMind published the much anticipated, detailed methodology underlying the latest version of AlphaFold – the UK-based science company's powerful AI system that blew away its rivals in the latest major competition to predict the 3D structure of proteins. AlphaFold's machine learning methodology has been applied to predict structures for almost 99% of human proteins which have now been made publicly available. In this long read, I reflect on the significance of these developments for fundamental research and drug discovery. I wrote this as the ICR celebrates the 10th anniversary of its AI-enabled drug discovery knowledgebase canSAR – which features multiple approaches to predicting'druggability' as an aid to selecting drug targets and accelerating drug discovery. The coronavirus pandemic has, understandably, soaked up a lot of bandwidth when it comes to science news – but one particular non-Covid science story was able to cut through and hit the headlines in the UK and around the world. On 30 November 2020 it was announced that DeepMind – a subsidiary of Google's parent company Alphabet focusing on artificial intelligence – had made what was hailed as a huge leap towards solving one of biology's greatest remaining challenges: the ability to predict the correct, three-dimensional structures of proteins based on their constituent, one-dimensional amino acid sequences. The announcement attracted huge interest, but the expert community has been waiting for the peer-reviewed science publication. The AI methodology has now been published in the leading journal Nature and this was followed rapidly by a second Nature paper from DeepMind and collaborators at the European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), which reports the application of the most recent AlphaFold machine learning system to predict the 3D structures at scale for almost the entire human proteome – 98.5% of human proteins.