Section: New Results

Inverse Protein Folding Problem via Quadratic Programming

Participants : Mikhail Karasikov, Sergei Grudinin.

We presented 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.

Figure 20. Approximate energy optimum for different relaxations computed on the test set