The Protein Sequence Design Problem in Canonical Model on 2D and 3D Lattices

In this paper we investigate the protein sequence design (PSD) problem (also known as the inverse protein folding problem) under the Canonical model 4 on 2D and 3D lattices [12, 25]. The Canonical model is specified by (i) a geometric representation of a target protein structure with amino acid residues via its contact graph, (ii) a binary folding code in which the amino acids are classified as hydrophobic (H) or polar (P), (iii) an energy function Φ defined in terms of the target structure that should favor sequences with a dense hydrophobic core and penalize those with many solvent-exposed hydrophobic residues (in the Canonical model, the energy function Φ gives an H-H residue contact in the contact graph a value of −1 and all other contacts a value of 0), and (iv) to prevent the solution from being a biologically meaningless all H sequence, the number of H residues in the sequence S is limited by fixing an upper bound λ on the ratio between H and P amino acids. The sequence...

• Type: Conference
• Year: 2004
• Where: CPM
• Authors: Piotr Berman, Bhaskar DasGupta, Dhruv Mubayi, Robert H. Sloan, György Turán, Yi Zhang
• Keywords: Canonical Model, CPM 2004, Global Energy Minima, PSD Problem