AlphaFold is an artificial intelligence program developed by Google’s DeepMind which performs predictions of protein structure. The program is designed as a deep learning system.
AlphaFold AI software has been notable in two major versions. A team of researchers that used AlphaFold 1 (2018) placed first in the overall rankings of the 13th Critical Assessment of Techniques for Protein 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 organizers, 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 CASP 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.
DeepMind’s new protein-folding A.I. is already helping in the fight against COVID-19.
AlphaFold 2’s results at CASP were described as “astounding” and transformational. Some researchers criticized the AlphaFold team for not making the method publicly available for independent verification and reimplementation and noticed that the reasons for its success still need to be understood. Nevertheless, there has been widespread respect for the technical achievement.
Artificial intelligence has just solved one of biology’s most vexing challenges: how to determine the three-dimensional shape of a protein. DeepMind, the London-based A.I. company that is owned by Google-parent Alphabet, has created an A.I. system it calls AlphaFold 2 that uses a protein’s DNA sequence to predict its folded shape, frequently to within an atom’s width of accuracy. Previously, this could be done only through time-consuming and expensive experiments. (Read more about how DeepMind accomplished this goal here.) In the future, the breakthrough is likely to speed the development of new medicines for everything from malaria to cancer. But AlphaFold 2 is already having an impact on the fight against today’s most pressing global health scourge: the COVID-19 pandemic.
Almost as soon as fears arose that a novel coronavirus was circulating in Wuhan, China, with the potential to become a global pandemic, DeepMind, like many companies, wanted to do something to help. The potential to use AlphaFold 2, DeepMind’s still-under-wraps new A.I. system, to gain insights into the virus was clear. But the system, which was being prepared for its debut in a global competition on protein structure prediction that was still months away, had not yet been fully tested.
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