Structure-approximating inverse protein folding problem in the 2D HP model. |
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Authors: | Arvind Gupta Ján Manuch Ladislav Stacho |
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Institution: | School of Computing Science, Simon Fraser University, Burnaby BC, Canada. |
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Abstract: | The inverse protein folding problem is that of designing an amino acid sequence which has a particular native protein fold. This problem arises in drug design where a particular structure is necessary to ensure proper protein-protein interactions. In this paper, we show that in the 2D HP model of Dill it is possible to solve this problem for a broad class of structures. These structures can be used to closely approximate any given structure. One of the most important properties of a good protein (in drug design) is its stability--the aptitude not to fold simultaneously into other structures. We show that for a number of basic structures, our sequences have a unique fold. |
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