Inverse protein folding in 2D HP mode (extended abstract)

Proc IEEE Comput Syst Bioinform Conf. 2004:311-8.

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.

MeSH terms

  • Algorithms*
  • Computer Simulation
  • Drug Design*
  • Hydrogen Bonding
  • Models, Chemical*
  • Models, Molecular*
  • Protein Conformation
  • Protein Denaturation
  • Protein Folding
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*