Approximate Protein Folding in the HP Side Chain Model on Extended Cubic
Lattices
One of the most important open problems in computational molecular
biology is the prediction of the conformation of a protein based on
its amino acid sequence.
In this paper, we design approximation algorithms for structure
prediction in the so-called HP side chain model.
The major drawback of the standard HP side chain model is the
bipartiteness of the cubic lattice.
To eliminate this drawback, we introduce the extended cubic lattice
which extends the cubic lattice by diagonals in the plane.
For this lattice, we present two linear algorithms with approximation
ratios of 59/70 and 37/42, respectively.
The second algorithm is designed for a `natural' subclass of proteins,
which covers more than 99.5% of all sequenced proteins.
This is the first time that a protein structure prediction algorithm is
designed for a `natural' subclass of all combinatoric possible
sequences.
