AlphaFold facts for kids

AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure. The program is designed as a deep learning system.

AlphaFold software has had three major versions. A team of researchers that used AlphaFold 1 (2018) placed first in the overall rankings of the 13th Critical Assessment of Structure Prediction (CASP) in December 2018. The program was particularly successful at predicting the most accurate structure for targets rated as the most difficult by the competition organisers, where no existing template structures were available from proteins with a partially similar sequence. A team that used AlphaFold 2 (2020) repeated the placement in the CASP14 competition in November 2020. The team achieved a level of accuracy much higher than any other group. It scored above 90 for around two-thirds of the proteins in CASP's global distance test (GDT), a test that measures the degree to which a computational program predicted structure is similar to the lab experiment determined structure, with 100 being a complete match, within the distance cutoff used for calculating GDT.

AlphaFold 2's results at CASP14 were described as "astounding" and "transformational". Some researchers noted that the accuracy is not high enough for a third of its predictions, and that it does not reveal the mechanism or rules of protein folding for the protein folding problem to be considered solved. Nevertheless, there has been widespread respect for the technical achievement, and analysis suggests that AlphaFold 2 is accurate enough to predict even single-mutation effects. On 15 July 2021 the AlphaFold 2 paper was published in Nature as an advance access publication alongside open source software and a searchable database of species proteomes. Alternatives to AlphaFold have emerged, such as ESMFold, OmegaFold, RoseTTAFold, IntFOLD, and RaptorX. AlphaFold 3 was announced on 8 May 2024. Besides the improved accuracy on protein folding, it can also predict the structure and interactions of DNA, RNA, and of some ligands and ions.

Applications

AlphaFold has been used to predict structures of proteins of SARS-CoV-2, the causative agent of COVID-19. The structures of these proteins were pending experimental detection in early 2020. Results were examined by the scientists at the Francis Crick Institute in the United Kingdom before release into the larger research community. The team also confirmed accurate prediction against the experimentally determined SARS-CoV-2 spike protein that was shared in the Protein Data Bank, an international open-access database, before releasing the computationally determined structures of the under-studied protein molecules. The team acknowledged that although these protein structures might not be the subject of ongoing therapeutical research efforts, they will add to the community's understanding of the SARS-CoV-2 virus. Specifically, AlphaFold 2's prediction of the structure of the ORF3a protein was very similar to the structure determined by researchers at University of California, Berkeley using cryo-electron microscopy. This specific protein is believed to assist the virus in breaking out of the host cell once it replicates. This protein is also believed to play a role in triggering the inflammatory response to the infection.

Images for kids

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  Amino-acid chains, known as polypeptides, fold to form a protein.

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  AlphaFold 2 performance, experiments, and architecture

See also

In Spanish: AlphaFold para niños