A Quasi-physical Algorithm for the Structure Optimization in an Off-lattice Protein Model
- Author:
Liu JING-FA
1
;
Huang WEN-QI
Author Information
1. 华中科技大学
- Keywords:
protein folding;
off-lattice model;
quasi-physical algorithm;
off-trap strategy
- From:
Genomics, Proteomics & Bioinformatics
2006;4(1):61-66
- CountryChina
- Language:Chinese
-
Abstract:
In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain.A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers.In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins.
