A replica exchange Monte Carlo algorithm for protein folding in the HP model

Background: The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be -hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC) method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP) lattice models. Results: We demonstrate that REMC is highly effective for solving instances of the square (2D) and cubic (3D) HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-t...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Chris Thachuk, Alena Shmygelska, Holger H. Hoos
• Keywords: Ab Initio Protein, BMCBI 2007, Protein, State-of-the-art Methods