Protein Folding in Hydrophobic-Polar Lattice Model: A Flexible Ant-Colony Optimization Approach

Abstract

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms.

Biochemical localization of a protein involved in synthesis of Gluconacetobacter hansenii cellulose

“…This is consistent with our unpublished small angle X-ray scattering and analytical ultracentrifugation results. Given the dimensions from the X-ray crystal structure of AcsD, (Hu et al 2008) and our own SAXS data (unpublished data), the diameter of the central pore of AcsD tetramer is in the range 9-13 nm, which indicates that one AcsD octatmer can fit in the periplasmic space which is known to be an expandable gel of 10-25 nm width (Graham et al 1991a, b). The crystal structure of AcsD also shows that the central pore of AcsD is 3 nm.…”

“…For it to function as a channel necessitates that some part of AcsD is associated with AcsAB and AcsC. The crystal structure provides a model of how AcsD would provide such a channel (Hu et al 2008). The unit cell of AcsD is two tetrameric rings stacked on top of each other.…”

“…Database searches give very little information with respect to proteins homologous to AcsD. Though the structure of AcsD has been recently elucidated by X-ray diffraction pattern (Hu et al 2008), absence of information about the location of the protein makes it difficult to understand its interactions with the other proteins of the operon, as well as the precise mechanism by which the protein contributes to the process of cellulose extrusion.…”

Implementation of Object Oriented Approach to Efficient Task Scheduling in Grid Computing with Modified Ant Algorithm

“…In grid, resources are distributed, heterogeneous, dynamic and instability. Yi Li et.al proposed [11], which is a new heuristic algorithm and based on the behavior of real ants. When the blind insects, such as ants look for food, the moving ant lays some pheromone on the ground, thus making the path it followed by a trail of this substance.…”

A clustering-based adaptive parameter control method for continuous ant colony optimization

“…Because of its strong searching ability and robustness, ACO has been widely and successfully applied in solving problems such as the traveling salesman problem [1] [2], scheduling problem [3] [4], protein folding problem [5], and other problems [6] [7]. Recently several extended ACO algorithms have also been proposed to deal with continuous optimization problems [8] [9].…”