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A Bearing-Only Pattern Formation Algorithm for Swarm Robotics Read chapter Read first chapter

2016 | OriginalPaper | Chapter

A Study of Archiving Strategies in Multi-objective PSO for Molecular Docking

Authors : José García-Nieto, Esteban López-Camacho, María Jesús García Godoy, Antonio J. Nebro, Juan J. Durillo, José F. Aldana-Montes

Published in: Swarm Intelligence

Publisher: Springer International Publishing

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Abstract

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-objective swarm-intelligence algorithm has shown a remarkable performance. SMPSO is characterized by having an external archive used to store the non-dominated solutions and also as the basis of the leader selection strategy. In this paper, we analyze several SMPSO variants based on different archiving strategies in the scope of a benchmark of molecular docking instances. Our study reveals that the SMPSOhv, which uses an hypervolume contribution based archive, shows the overall best performance.

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previous chapter A New Continuous Model for Segregation Implemented and Analyzed on Swarm Robots
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Footnotes
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Metadata
Title
A Study of Archiving Strategies in Multi-objective PSO for Molecular Docking
Authors
José García-Nieto
Esteban López-Camacho
María Jesús García Godoy
Antonio J. Nebro
Juan J. Durillo
José F. Aldana-Montes
Copyright Year
2016
Book
Swarm Intelligence

Print ISBN: 978-3-319-44426-0

Electronic ISBN: 978-3-319-44427-7

Copyright Year: 2016

DOI
https://doi.org/10.1007/978-3-319-44427-7_4

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