title: The Noncompacted Folding of Proteins by Modified Elastic Net Algorithm.
abstract: In this article, a protein sequence of length n is embedded in a two-dimensional lattice with m (>n) points. Thus the obtained minimal energy configurations are expected to have flexible shapes in contrast to the compact rectangular conformations. To fulfill this extension, the elastic net algorithm is modified to deal with the difficulty brought by the unsymmetrical relationship between amino acids and lattice points. New set partition strategy in the embedding phase is introduced, and two local search methods are applied to overcome the multimapping phenomena. Several HP benchmark examples with up to 48 amino acids are tested to verify the effectiveness of the proposed approach.
authors.affiliation: Department of Mathematics, College of Science, Nanjing University of Aeronautics and Astronautics , Nanjing, China .
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Guo
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D057927:Hydrophobic and Hydrophilic Interactions; D008956:Models, Chemical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: HP lattice model; elastic net algorithm; local search; noncompacted shape; protein folding problem