Inverse protein folding in 2D HP mode (extended 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.
Gupta
Arvind
A
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada. arvind@mitacs.ca
Manuch
Ján
J
Stacho
Ladislav
L
D000465:Algorithms; D003198:Computer Simulation; D015195:Drug Design; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*