Structure-approximating inverse protein folding problem in the 2D HP model.
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.
Gupta
Arvind
A
School of Computing Science, Simon Fraser University, Burnaby BC, Canada.
Manuch
Ján
J
Stacho
Ladislav
L
D019295:Computational Biology; D015195:Drug Design; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics