AlphaFold- The The Hindu-02-08-2022



DeepMind, a company based in London and owned by Google, announced this week that it had predicted the threedimensional structures of more than 200 million proteins using AlphaFold. This is the entire protein universe known to scientists today.


AlphaFold is an AIbased protein structure prediction tool. It is based on a computer system called deep neural network. Inspired by the human brain, neural networks use a large amount of input data and provides the desired output exactly like how a human brain would. The real work is done by the black box between the input and the output layers, called the hidden networks.
AlphaFold is fed with protein sequences as input. When protein sequences enter through one end, the predicted threedimensional structures come out through the other. It is like a magician pulling a rabbit out of a hat.

How does AlphaFold work?

The first step uses the available structures of 1,70,000 proteins in the Protein Data Bank (PDB) to train the computer model. Then, it uses the results of that training to learn the structural predictions of proteins not in the PDB. Once that is done, it uses the highaccuracy predictions from the first step to retrain and relearn to gain higher accuracy of the earlier predictions.

What are the implications of this development?

1.AlphaFold has already helped hundreds of scientists accelerate their discoveries in vaccine and drug development since the first public release of the database nearly a year back.
2.The development of AlphaFold is a watershed movement in science and structural biology in particular.
3.Proteins are the business ends of biology, meaning proteins carry out all the functions inside a living cell.
4.Scientists predict protein structures using xray crystallography, nuclear magnetic resonance spectroscopy, or cryogenic electron microscopy.

What does this development mean for India?

It needs to quickly take advantage of the AlphaFold database and learn how to use the structures to design better vaccines and drugs.
Understanding the accurate structures of COVID19 virus proteins in days rather than years will accelerate vaccine and drug development against the virus.
India will also need to speed up its implementation of publicprivate partnerships in the sciences.
The publicprivate partnership between the European Molecular Biology Laboratory’s European Bioinformatics Institute and DeepMind made the 25terabyte AlphaFold dataset accessible to everyone in the scientific community at no cost.

Conclusion :

AlphaFold is a once in a generation advance, predicting protein structures with incredible speed and precision. AlphaFold 1 proved that neural networks posses the complexity required in order to be capable of modeling the protein folding mechanism. AlphaFold 2 further improves accuracy by using a more representative internal representation and embedding equivariance knowledge in the model.

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