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 Arvind Gupta

Title of talk:
Inverse Protein Folding for Constructible Structures*

December 11, 2003

School of Computing Science, SFU


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Talk Summary:
Dill and others introduced the Hydrophobic-Polar model for amino-acid interactions to capture the ion bonding in proteins as a way to model the protein folding problem. They suggested working on the 2-D lattice so as to gain a deeper understanding of the structures that may arise. Subsequently a number of authors began studying the inverse protein folding problem. Here, a native protein fold is specified and an amino acid sequence is required that exhibits this fold. Furthermore, the sequence should be robust in that it should not have any other minimum energy fold. Working on this 2-D lattice, we show that given a structure it is possible to design an amino acid sequence whose native fold under the HP model closely approximates the structure. Proving robustness is more challenging. However we show that for two base structures the stronger robustness condition holds. We conjecture that using these base structures it is possible to show robustness for all our structures.

*Joint with Jano Manuch and Ladislav Stacho, Simon Fraser University.


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