Paper Info
Title
Multi-objective Metaheuristics for a Flexible Ligand-Macromolecule Docking Problem in Computational Biology.
Abstract
The problem of molecular docking focuses on minimizing the binding energy of a complex composed by a ligand and a receptor. In this paper, we propose a new approach based on the joint optimization of three conflicting objectives: Einter that relates to the ligand-receptor affinity, the Eintra characterizing the ligand deformity and the RMSD score (Root Mean Square Deviation), which measures the difference of atomic distances between the co-crystallized ligand and the computed ligand. In order to deal with this multi-objective problem, three different metaheuristic solvers (SMPSO, MOEA/D and MPSO/D) are used to evolve a numerical representation of the ligand's conformation. An experimental benchmark is designed to shed light on the comparative performance of these multi-objective heuristics, comprising a set of HIV-proteases/inhibitors complexes where flexibility was applied. The obtained results are promising, and pave the way towards embracing the proposed algorithms for practical multi-criteria in the docking problem.
Year
DOI
Venue
2018
10.1007/978-3-319-99626-4_32
Studies in Computational Intelligence
Keywords
Field
DocType
Molecular docking,Multi-objective optimization,Flexibility modeling,SMPSO,MOEA/D,MPSO/D
Docking (molecular),Macromolecule,Ligand,Computer science,Docking (dog),Algorithm,Multi-objective optimization,Heuristics,Root-mean-square deviation,Metaheuristic
Conference
Volume
ISSN
Citations 
798
1860-949X
0
PageRank 
References 
Authors
0.34
13
5
Name
Order
Citations
PageRank
Esteban López-Camacho1295.13
María Jesús García-Godoy2345.57
Javier Del Ser371287.90
Antonio J. Nebro4111854.62
José Francisco Aldana Montes527636.81