Dataset Information

Biochemical systems identification by a random drift particle swarm optimization approach.

ABSTRACT:

Background

Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signalling pathways. The problem is stated as a data-driven nonlinear regression problem, which is converted into a nonlinear programming problem with many nonlinear differential and algebraic constraints. Due to the typical ill conditioning and multimodality nature of the problem, it is in general difficult for gradient-based local optimization methods to obtain satisfactory solutions. To surmount this limitation, many stochastic optimization methods have been employed to find the global solution of the problem.

Results

This paper presents an effective search strategy for a particle swarm optimization (PSO) algorithm that enhances the ability of the algorithm for estimating the parameters of complex dynamic biochemical pathways. The proposed algorithm is a new variant of random drift particle swarm optimization (RDPSO), which is used to solve the above mentioned inverse problem and compared with other well known stochastic optimization methods. Two case studies on estimating the parameters of two nonlinear biochemical dynamic models have been taken as benchmarks, under both the noise-free and noisy simulation data scenarios.

Conclusions

The experimental results show that the novel variant of RDPSO algorithm is able to successfully solve the problem and obtain solutions of better quality than other global optimization methods used for finding the solution to the inverse problems in this study.

SUBMITTER: Sun J

PROVIDER: S-EPMC4158603 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

Biochemical systems identification by a random drift particle swarm optimization approach.

Sun Jun J Palade Vasile V Cai Yujie Y Fang Wei W Wu Xiaojun X

BMC bioinformatics 20140516

<h4>Background</h4>Finding an efficient method to solve the parameter estimation problem (inverse problem) for nonlinear biochemical dynamical systems could help promote the functional understanding at the system level for signalling pathways. The problem is stated as a data-driven nonlinear regression problem, which is converted into a nonlinear programming problem with many nonlinear differential and algebraic constraints. Due to the typical ill conditioning and multimodality nature of the pro ...[more]

PMID: 25078435

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Project description:BACKGROUND:Protein-ligand docking has emerged as a particularly important tool in drug design and development, and flexible ligand docking is a widely used method for docking simulations. Many docking software packages can simulate flexible ligand docking, and among them, Autodock is widely used. Focusing on the search algorithm used in Autodock, many new optimization approaches have been proposed over the last few decades. However, despite the large number of alternatives, we are still lacking a search method with high robustness and high performance. RESULTS:In this paper, in conjunction with the popular Autodock software, a novel hybrid version of the random drift particle swarm optimization (RDPSO) algorithm, called diversity-guided Lamarckian RDPSO (DGLRDPSO), is proposed to further enhance the performance and robustness of flexible ligand docking. In this algorithm, a novel two-phase diversity control (2PDC) strategy and an efficient local search strategy are used to improve the search ability and robustness of the RDPSO algorithm. By using the PDBbind coreset v.2016 and 24 complexes with apo-structures, the DGLRDPSO algorithm is compared with the Lamarckian genetic algorithm (LGA), Lamarckian particle swarm optimization (LPSO) and Lamarckian random drift particle swarm optimization (LRDPSO). The experimental results show that the 2PDC strategy is able to enhance the robustness and search performance of the proposed algorithm; for test cases with different numbers of torsions, the DGLRDPSO outperforms the LGA and LPSO in finding both low-energy and small-RMSD docking conformations with high robustness in most cases. CONCLUSION:The DGLRDPSO algorithm has good search performance and a high possibility of finding a conformation with both a low binding free energy and a small RMSD. Among all the tested algorithms, DGLRDPSO has the best robustness in solving both holo- and apo-structure docking problems with different numbers of torsions, which indicates that the proposed algorithm is a reliable choice for the flexible ligand docking in Autodock software.

Project description:BACKGROUND:Protein-ligand docking programs are routinely used in structure-based drug design to find the optimal binding pose of a ligand in the protein's active site. These programs are also used to identify potential drug candidates by ranking large sets of compounds. As more accurate and efficient docking programs are always desirable, constant efforts focus on developing better docking algorithms or improving the scoring function. Recently, chaotic maps have emerged as a promising approach to improve the search behavior of optimization algorithms in terms of search diversity and convergence speed. However, their effectiveness on docking applications has not been explored. Herein, we integrated five popular chaotic maps-logistic, Singer, sinusoidal, tent, and Zaslavskii maps-into PSOVina[Formula: see text], a recent variant of the popular AutoDock Vina program with enhanced global and local search capabilities, and evaluated their performances in ligand pose prediction and virtual screening using four docking benchmark datasets and two virtual screening datasets. RESULTS:Pose prediction experiments indicate that chaos-embedded algorithms outperform AutoDock Vina and PSOVina in ligand pose RMSD, success rate, and run time. In virtual screening experiments, Singer map-embedded PSOVina[Formula: see text] achieved a very significant five- to sixfold speedup with comparable screening performances to AutoDock Vina in terms of area under the receiver operating characteristic curve and enrichment factor. Therefore, our results suggest that chaos-embedded PSOVina methods might be a better option than AutoDock Vina for docking and virtual screening tasks. The success of chaotic maps in protein-ligand docking reveals their potential for improving optimization algorithms in other search problems, such as protein structure prediction and folding. The Singer map-embedded PSOVina[Formula: see text] which is named PSOVina-2.0 and all testing datasets are publicly available on https://cbbio.cis.umac.mo/software/psovina .

Dataset Information

Biochemical systems identification by a random drift particle swarm optimization approach.

Background

Results

Conclusions

Publications

Biochemical systems identification by a random drift particle swarm optimization approach.

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