Inverse Protein Folding in 2D HP Mode (Extended Abstract)

Authors:
Arvind Gupta;Jan Manuch;Ladislav Stacho
Affiliations:
Simon Fraser University;Simon Fraser University;Simon Fraser University
Venue:
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Year:
2004

Citing 3
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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 is its stability 驴 the aptitude not to fold simultanously into other structures. We show that for a number of basic structures, our sequences have a unique fold.