embio – cambridge particle swarm optimization applied to automated docking automated docking of a...
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![Page 1: EMBIO – Cambridge Particle Swarm Optimization applied to Automated Docking Automated docking of a ligand to a macromolecule Particle Swarm Optimization](https://reader036.vdocuments.site/reader036/viewer/2022062421/56649d3e5503460f94a16e25/html5/thumbnails/1.jpg)
EMBIO – Cambridge
Particle Swarm Optimization applied to Automated Docking
Automated docking of a ligand to a macromolecule
Particle Swarm Optimization Multi-objective PSO + Clustering Docking experiments Conclusion
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EMBIO – Cambridge
Automated Docking Predict binding of a ligand molecule to
a receptor macromolecule Minimize resulting binding energy
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EMBIO – Cambridge
Energy Evaluation
[Morris et al.]
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EMBIO – Cambridge
Autodock 3.05 Determine energies using trilinear
interpolation on precalculated grid maps
Minimize docking energy with various optimization techniques Simulated Annealing Genetic Algorithm with Local Search
Sum of energies is minimized
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EMBIO – Cambridge
Particle Swarm Optimization
Multi-dimensional, numerical optimization by a swarm of particles
Each particle has current position ,best position and velocity
Attracted by personal best positionand neighbourhood best position
![Page 6: EMBIO – Cambridge Particle Swarm Optimization applied to Automated Docking Automated docking of a ligand to a macromolecule Particle Swarm Optimization](https://reader036.vdocuments.site/reader036/viewer/2022062421/56649d3e5503460f94a16e25/html5/thumbnails/6.jpg)
EMBIO – Cambridge
PSO Algorithm
![Page 7: EMBIO – Cambridge Particle Swarm Optimization applied to Automated Docking Automated docking of a ligand to a macromolecule Particle Swarm Optimization](https://reader036.vdocuments.site/reader036/viewer/2022062421/56649d3e5503460f94a16e25/html5/thumbnails/7.jpg)
EMBIO – Cambridge
Clustering Particles are clustered into K separate
swarm
K-means Clustering m data-vectors are clustered into k
clusters Iteratively calculate centroids of each
cluster
![Page 8: EMBIO – Cambridge Particle Swarm Optimization applied to Automated Docking Automated docking of a ligand to a macromolecule Particle Swarm Optimization](https://reader036.vdocuments.site/reader036/viewer/2022062421/56649d3e5503460f94a16e25/html5/thumbnails/8.jpg)
EMBIO – Cambridge
Multiple Objectives Optimize ,
simultaneously Find dominating solutions
Non-Dominated Front
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EMBIO – Cambridge
Clust-MPSO Update personal best position
Each swarm has non-dominated front is dominated if no particle is in Dominated swarms are relocated
Neighbourhood best particle Picked for several iterations
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EMBIO – Cambridge
![Page 11: EMBIO – Cambridge Particle Swarm Optimization applied to Automated Docking Automated docking of a ligand to a macromolecule Particle Swarm Optimization](https://reader036.vdocuments.site/reader036/viewer/2022062421/56649d3e5503460f94a16e25/html5/thumbnails/11.jpg)
EMBIO – Cambridge
1hvr Docking
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EMBIO – Cambridge
4cha Docking
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EMBIO – Cambridge
Convergence – 1hvr
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EMBIO – Cambridge
Convergence – 4cha
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EMBIO – Cambridge
Conclusions Application of PSO to Automated
Docking Optimization of two objectives Clustering to divide the search space