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Unfolding the mystery of proteins

U.S. Patent #8,423,339: Visual analysis of a protein folding process
Patent Issued: April 16, 2013
Inventors: Laxmi Parida, Ruhong Zhou

What is patent #8,423,339? By Laxmi Parida, Manager, IBM Computational Genomics Group.

Proteins do just about everything in our cells. And those functions, from hormones transport to muscle contraction and much more, are determined by the order and arrangement of protein building blocks, amino acids. Patent #8,423,339 gives scientists a way to break down that folding process – which happens in the fraction of a blink of an eye – to understand why proteins fold (and mis-fold) into certain shapes.

In nature, amino acids in a cell bind together and form a specifically shaped protein. How does this happen? We’re still trying to figure that out. It even has its own paradox, Levinthal’s Paradox, stating that the folding can’t be random (even though it seems that way) because it’s too complicated.

We know what proteins are made of, but since we can’t see how proteins fold in nature, we have to simulate them. And we’ve been simulating protein folding since before Blue Gene/L in 1999. Our patent uses the data from these simulations to find and understand the paths the amino acids take during the folding process.

The tough thing about finding patterns in the process of protein folding is that everything in the data could potentially be a pattern. So, we have to hunt for informative combinations of values that surface again and again – not necessarily in tandem, in the process of folding.

Visualization of the varying landscape of patterns as a protein folds


These simulations that create 3D models generate massive amounts of data. But our pattern discovery technique works at the level of the simulator, from workstation to supercomputer. It efficiently combs the data to find these invariant combinatorial subsets, which could provide valuable insight into the folding process.

Knowing how proteins fold or why they mis-fold will help us understand how cells work and don’t work. Say, in the case of bovine spongiform encephalopathy (mad cow disease). By understanding the process that created the mis-shapen prion, we could possibly cure or eradicate it, or any other such disease.

IBM has led in total U.S. patents for 21 year in a row in 2013. Read more about patents like #8,423,339, here.

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