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Updated: Aug 13, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Inverse protein folding in 2D HP mode (extended abstract)
Arvind Gupta1, Ján Manuch, Ladislav Stacho
1School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. arvind@mitacs.ca
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 -- the aptitude not to fold simultanously into other structures. We show that for a number of basic structures, our sequences have a unique fold.
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