AlphaFold2

A deeper look at AlphaFold2 and its neural architectureIllustration of protein sequence to shape. In white the original protein, in rainbow the AlphaFold predicted protein (Illustration by the author)In this series of articles, I will go through protein folding and deep learning models such as AlphaFold, OmegaFold, and ESMFold. We will start with AlphaFold2!Proteins are molecules that perform most of the biochemical functions in living organisms. They are involved in digestion (enzymes), structural processes (keratin —…

Use Alphafold2 with limited computational resourcesPhoto by Luke Jones on UnsplashIt is no longer news that one of the steepest challenges in biology has been leveled by a London-based artificial intelligence outfit — DeepMind. They won the Critical Assessment of protein-Structure Prediction 14 edition (CASP14) with a ground truth score of 90. DeepMind proceeded to publish a landmark paper in the summer of 2021.DeepMind named their protein-folding platform AlphaFold (updated version —AlphaFold v2.3.0 at the time of…

DeepMind promised us a revolution. Did it happen?image by Greg Rakozy at unsplash.comA year ago, AlphaFold2 was published in Nature. AlphaFold was presented during CASP13 (a competition where the goal is to predict the structure of proteins whose structure has been obtained but not yet published) where it outperformed the other competitors but without causing a stir. During the subsequent CASP14 competition, AlphaFold2 defeated not only all other competitors but the results predicted by the algorithm were similar to those…

AI is reshaping research in biology and opening new frontiers in therapyImage generated with OpenAI Dall-E 2 and then modified by the author (using the protein from here)Proteins are the fundamental building blocks of life, and are involved in any process in the cell. Their unique structures and diverse functions allow them to perform any task in the cell. DNA and RNA can be seen as the ROM and RAM memory.Understanding the structure and the functions of proteins takes considerable effort from the scientific community.…