Title: Inverse Protein Folding Problem via Quadratic Programming,
Abstract: This paper presents a method of reconstruction a primary structure of a
protein that folds into a given geometrical shape. This method predicts the
primary structure of a protein and restores its linear sequence of amino acids
in the polypeptide chain using the tertiary structure of a molecule. Unknown
amino acids are determined according to the principle of energy minimization.
This study represents inverse folding problem as a quadratic optimization
problem and uses different relaxation techniques to reduce it to the problem of
convex optimizations. Computational experiment compares the quality of these
approaches on real protein structures.