Flexible protein-ligand docking using particle swarm optimization

2005 ◽  
Author(s):  
Bo-Fu Liu ◽  
Hung-Ming Chen ◽  
Hui-Ling Huang ◽  
Shiow-Fen Hwang ◽  
Shinn-Ying Ho
Keyword(s):  
Particle Swarm Optimization ◽  
Particle Swarm ◽  
Ligand Docking ◽  
Swarm Optimization ◽  
Flexible Protein

scholarly journals PSOVina: The hybrid particle swarm optimization algorithm for protein–ligand docking

2015 ◽  
Vol 13 (03) ◽  
pp. 1541007 ◽  
Author(s):  
Marcus C. K. Ng ◽  
Simon Fong ◽  
Shirley W. I. Siu
Keyword(s):  
Particle Swarm Optimization ◽  
Virtual Screening ◽  
Particle Swarm ◽  
Ligand Docking ◽  
Conformational Search ◽  
Search Problem ◽  
Data Set ◽  
Swarm Optimization ◽  
Screening Experiments ◽  
Hybrid Particle Swarm Optimization

Protein–ligand docking is an essential step in modern drug discovery process. The challenge here is to accurately predict and efficiently optimize the position and orientation of ligands in the binding pocket of a target protein. In this paper, we present a new method called PSOVina which combined the particle swarm optimization (PSO) algorithm with the efficient Broyden–Fletcher–Goldfarb–Shannon (BFGS) local search method adopted in AutoDock Vina to tackle the conformational search problem in docking. Using a diverse data set of 201 protein–ligand complexes from the PDBbind database and a full set of ligands and decoys for four representative targets from the directory of useful decoys (DUD) virtual screening data set, we assessed the docking performance of PSOVina in comparison to the original Vina program. Our results showed that PSOVina achieves a remarkable execution time reduction of 51–60% without compromising the prediction accuracies in the docking and virtual screening experiments. This improvement in time efficiency makes PSOVina a better choice of a docking tool in large-scale protein–ligand docking applications. Our work lays the foundation for the future development of swarm-based algorithms in molecular docking programs. PSOVina is freely available to non-commercial users at http://cbbio.cis.umac.mo .

Smart teaching mode based on particle swarm image recognition and human-computer interaction deep learning

2020 ◽  
Vol 39 (4) ◽  
pp. 5699-5711
Author(s):  
Shirong Long ◽  
Xuekong Zhao
Keyword(s):  
Feature Extraction ◽  
Particle Swarm Optimization ◽  
Deep Learning ◽  
Real Time ◽  
Image Recognition ◽  
Particle Swarm ◽  
Learning Technology ◽  
Search Performance ◽  
Swarm Optimization ◽  
Teaching Mode

The smart teaching mode overcomes the shortcomings of traditional teaching online and offline, but there are certain deficiencies in the real-time feature extraction of teachers and students. In view of this, this study uses the particle swarm image recognition and deep learning technology to process the intelligent classroom video teaching image and extracts the classroom task features in real time and sends them to the teacher. In order to overcome the shortcomings of the premature convergence of the standard particle swarm optimization algorithm, an improved strategy for multiple particle swarm optimization algorithms is proposed. In order to improve the premature problem in the search performance algorithm of PSO algorithm, this paper combines the algorithm with the useful attributes of other algorithms to improve the particle diversity in the algorithm, enhance the global search ability of the particle, and achieve effective feature extraction. The research indicates that the method proposed in this paper has certain practical effects and can provide theoretical reference for subsequent related research.

Sistem Kontrol Optimal Fuzzy-Particle Swarm Optimization

2018 ◽  
Vol 9 (1) ◽  
pp. 1-5
Author(s):  
Fachrudin Hunaini ◽  
Imam Robandi ◽  
Nyoman Sutantra
Keyword(s):  
Fuzzy Logic ◽  
Particle Swarm Optimization ◽  
Control System ◽  
Membership Function ◽  
Fuzzy Logic Control ◽  
Particle Swarm ◽  
Optimization Method ◽  
Swarm Optimization ◽  
Motion Error ◽  
Logic Control

Fuzzy Logic Control (FLC) is a reliable control system for controlling nonlinear systems, but to obtain optimal fuzzy logic control results, optimal Membership Function parameters are needed. Therefore in this paper Particle Swarm Optimization (PSO) is used as a fast and accurate optimization method to determine Membership Function parameters. The optimal control system simulation is carried out on the automatic steering system of the vehicle model and the results obtained are the vehicle's lateral motion error can be minimized so that the movement of the vehicle can always be maintained on the expected trajectory

Adaptive Inertia Weight Particle Swarm Optimization For Linear and Nonlinear Channel Equalization

2012 ◽  
Vol 3 (4) ◽  
pp. 1-4
Author(s):  
Diana D.C Diana D.C ◽  
◽  
Joy Vasantha Rani.S.P Joy Vasantha Rani.S.P ◽  
Nithya.T.R Nithya.T.R ◽  
Srimukhee.B Srimukhee.B
Keyword(s):  
Particle Swarm Optimization ◽  
Particle Swarm ◽  
Channel Equalization ◽  
Swarm Optimization ◽  
Inertia Weight ◽  
Linear And Nonlinear
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