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An Ant Colony Optimization Algorithm for the 2D HP Protein Folding Problem
- in Proc. 16th Canad. Conf. Artif. Intell
, 2002
"... The prediction of a protein's conformation from its aminoacid sequence is one of the most prominent problems in computational biology. Here, we focus on a widely studied abstraction of this problem, the two dimensional hydrophobic-polar (2D HP) protein folding problem. ..."
Abstract
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Cited by 9 (1 self)
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The prediction of a protein's conformation from its aminoacid sequence is one of the most prominent problems in computational biology. Here, we focus on a widely studied abstraction of this problem, the two dimensional hydrophobic-polar (2D HP) protein folding problem.
Parallel Ant Colony Optimization for 3D Protein Structure Prediction using the HP Lattice Model
"... The Protein Folding Problem studies the way in which a protein- a chain of amino acids- will ’fold ’ into its natural state. Predicting the way in which various proteins fold can be fundamental in developing treatments of diseases such as Alzeihmers and Systic Fibrosis. Classical solutions to calcul ..."
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to calculating the final conformation of a protein structure are resource-intensive. The Hydrophobic-Hydrophilic (HP) method is one way of simplifying the problem. We introduce a novel method of solving the HP protein folding problem in both two and three dimensions using Ant Colony Optimizations and a
Ant colony system approach for protein folding
- Proceedings of the International Multiconference on Computer Science and Information Technology. – 2008. – P
"... Abstract—The protein folding problem is a fundamental prob-lem in computational molecular biology and biochemical physics. The high resolution 3D structure of a protein is the key to the understanding and manipulating of its biochemical and cellular functions. All information necessary to fold a pro ..."
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Cited by 2 (0 self)
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problem simplified models such as hydrophobic-polar (HP) model have become one of the major tools for studying protein structure. Various optimization methods have been applied on folding problem including Monte Carlo methods, evolutionary algorithm, ant colony optimization algorithm. In this work we
An Improved Ant Colony Optimisation Algorithm for the 2D HP Protein Folding Problem
- HP Protein Folding Problem, Lecture
"... The prediction of a protein's structure from its amino-acid sequence is one of the most important problems in computational biology. In the current work, we focus on a widely studied abstraction of this problem, the 2-dimensional hydrophobic-polar (2D HP) protein folding problem. We present ..."
Abstract
-
Cited by 9 (2 self)
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The prediction of a protein's structure from its amino-acid sequence is one of the most important problems in computational biology. In the current work, we focus on a widely studied abstraction of this problem, the 2-dimensional hydrophobic-polar (2D HP) protein folding problem. We present
An improved ant colony . . .
- HP PROTEIN FOLDING PROBLEM, LECTURE
"... The prediction of a protein’s structure from its amino-acid sequence is one of the most important problems in computational biology. In the current work, we focus on a widely studied abstraction of this problem, the 2-dimensional hydrophobic-polar (2D HP) protein folding problem. We present an imp ..."
Abstract
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The prediction of a protein’s structure from its amino-acid sequence is one of the most important problems in computational biology. In the current work, we focus on a widely studied abstraction of this problem, the 2-dimensional hydrophobic-polar (2D HP) protein folding problem. We present
Enlighten – Research publications by members of the University of Glasgow http://eprints.gla.ac.uk Protein Folding in Hydrophobic-Polar Lattice Model: A Flexible Ant Colony Optimization Approach
, 2009
"... 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 protei ..."
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of proteins compared with other state-of-the-art algorithms. Key words — ant colony optimization, protein folding, hydrophobic-polar (HP) model, protein structure prediction
A concise overview of applications of ant colony optimization
- In Encyclopedia of Operations Research and Management Science
, 2011
"... Ant Colony Optimization (ACO) Despite being one of the youngest metaheuristics, the number of applications of ACO algorithms is very large. In principle, ACO can be applied to any combinatorial optimization problem for which some iterative solution construction mechanism can be conceived. Most app ..."
Abstract
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Cited by 1 (1 self)
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Ant Colony Optimization (ACO) Despite being one of the youngest metaheuristics, the number of applications of ACO algorithms is very large. In principle, ACO can be applied to any combinatorial optimization problem for which some iterative solution construction mechanism can be conceived. Most
A Hybrid Population based ACO Algorithm for Protein Folding
"... Abstract—A hybrid population based Ant Colony Optimization (ACO) algorithm PFold-P-ACO for protein folding in the HP model is proposed in this paper. This is the first population based ACO algorithm in the bioinformatics. It is shown experimentally that the algorithms achieves on nearly all test seq ..."
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Cited by 2 (0 self)
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Abstract—A hybrid population based Ant Colony Optimization (ACO) algorithm PFold-P-ACO for protein folding in the HP model is proposed in this paper. This is the first population based ACO algorithm in the bioinformatics. It is shown experimentally that the algorithms achieves on nearly all test
Prediction of Protein Backbone Based on the Sliced Lattice Model ∗
, 2008
"... In the past decades, a significant number of studies on the prediction of protein 3D tertiary structures have been extensively made. However, the folding rules, the core issue of protein structure prediction, still stay unsolved. Given a target protein with its primary amino acid sequence, the prote ..."
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lattice, which mixes coarse lattices with fine lattices. Our computation is based on the HP (Hydrophobic-Polar) model, combined with the constraint of disulfide bonds. The folding is optimized by using the ant colony optimization (ACO) algorithm. Our experimental results show that our prediction accuracy
When the Lowest Energy Does Not Induce Native Structures: Parallel Minimization of Multi-Energy Values by Hybridizing Searching Intelligences
, 2012
"... Background: Protein structure prediction (PSP), which is usually modeled as a computational optimization problem, remains one of the biggest challenges in computational biology. PSP encounters two difficult obstacles: the inaccurate energy function problem and the searching problem. Even if the lowe ..."
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energy function. By hybridizing the intelligences of parallel ant colonies and Monte Carlo Metropolis search, this paper demonstrates an implementation of our parallel approach for PSP. 16 classical instances were tested to show that the parallel approach is competitive for solving PSP problem
Results 1 - 10
of
15
