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What Is AlphaFold?

Context:

DeepMind, a company based in London and owned by Google, announced this week that it had predicted the three-dimensional structures of more than 200 million proteins using AlphaFold.

Relevance:

GS III- Science and Technology

Dimensions of the Article:

  1. What is AlphaFold?
  2. How does AlphaFold work?
  3. What are the implications of this development?
  4. Is AlphaFold one-of-a-kind tool in predicting protein structures?

What is AlphaFold?

  • AlphaFold is an AI-based 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 three-dimensional structures come out through the other. It is like a magician pulling a rabbit out of a hat.

How does AlphaFold work?

  • It uses processes based on “training, learning, retraining and relearning.”
  • 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 high-accuracy predictions from the first step to retrain and relearn to gain higher accuracy of the earlier predictions.
  • By using this method, AlphaFold has now predicted the structures of the entire 214 million unique protein sequences deposited in the Universal Protein Resource (UniProt) database.

What are the implications of this development?

  • Proteins are the business ends of biology, meaning proteins carry out all the functions inside a living cell.
    • Therefore, knowing protein structure and function is essential to understanding human diseases.
  •  Scientists predict protein structures using x-ray crystallography, nuclear magnetic resonance spectroscopy, or cryogenic electron microscopy.
    • These techniques are not just time-consuming, they often take years and are based mainly on trial-and-error methods.
  • The development of AlphaFold changes all of that. It is a watershed movement in science and structural biology in particular.
    • 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.

Is AlphaFold one-of-a-kind tool in predicting protein structures?

  • AlphaFold is neither flawless nor the only AI-based protein structure prediction tool.
  • RoseTTaFold, developed by David Baker at the University of Washington in Seattle, U.S., is another tool. Although less accurate than AlphaFold, it can predict the structure of protein complexes.
  • The development of AlphaFold is sure to make many scientists feel vulnerable, especially when they compare their efforts from years of hard work in the lab to that of a computer system. However, this is the time to adjust and take advantage of the new reality.

-Source: The Hindu


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September 2022
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