Tuning compilations by multi-objective optimization: Application to Apache web server

Martínez-Álvarez, Antonio; Cuenca-Asensi, Sergio; Ortíz, Andrés; Calvo-Zaragoza, Jorge; Tejuelo, Luis Alberto Vivas

doi:10.1016/j.asoc.2015.01.029

Cited by 10 publications

(7 citation statements)

References 20 publications

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“…The automated process also reduces human errors by using the web interface in generating alternative input files and parameters while interpreting the docking outcome [ 56 ]. SwissDock webserver is incorporated with the Apache web server, PHP (opensource technology) [ 59 ], which has dual Xeon E440 2.83 GHz at 1.7 Å and 16 GB. The docking procedures include minimizing at 100 steps steepest descent to remove any clashes inherent from adjusting the protein structure.…”

Section: Methodsmentioning

confidence: 99%

Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer’s Disease Therapy

et al. 2022

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In over a century since its discovery, Alzheimer’s disease (AD) has continued to be a global health concern due to its incurable nature and overwhelming increase among older people. In this paper, we give an overview of the efforts of researchers towards identifying potent BACE1 exosite-binding antibodies and allosteric inhibitors. Herein, we apply computer-aided drug design (CADD) methods to unravel the interactions of some proposed psychotic and meroterpenoid BACE1 allosteric site inhibitors. This study is aimed at validating the allosteric potentials of these selected compounds targeted at BACE1 inhibition. Molecular docking, molecular dynamic (MD) simulations, and post-MD analyses are carried out on these selected compounds, which have been experimentally proven to exhibit allosteric inhibition on BACE1. The SwissDock software enabled us to identify more than five druggable pockets on the BACE1 structural surface using docking. Besides the active site region, a melatonin derivative (compound 1) previously proposed as a BACE1 allostery inhibitor showed appreciable stability at eight different subsites on BACE1. Refinement with molecular dynamic (MD) simulations shows that the identified non-catalytic sites are potential allostery sites for compound 1. The allostery and binding mechanism of the selected potent inhibitors show that the smaller the molecule, the easier the attachment to several enzyme regions. This finding hereby establishes that most of these selected compounds failed to exhibit strong allosteric binding with BACE1 except for compound 1. We hereby suggest that further studies and additional identification/validation of other BACE1 allosteric compounds be done. Furthermore, this additional allosteric site investigation will help in reducing the associated challenges with designing BACE1 inhibitors while exploring the opportunities in the design of allosteric BACE1 inhibitors.

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Section: Methodsmentioning

confidence: 99%

Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer’s Disease Therapy

et al. 2022

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“…with multiple objectives [3,[19][20][21]. However, it has been logically proved by the well-known No-…”

Section: Most Of the Recent Algorithms Have Been Equipped With Suitabmentioning

confidence: 99%

Optimization of problems with multiple objectives using the multi-verse optimization algorithm

Mirjalili

Jangir²,

Mirjalili

et al. 2017

Knowledge-Based Systems

273

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This work proposes the multi-objective version of the recently proposed Multi-Verse Optimizer (MVO) called Multi-Objective Multi-Verse Optimizer (MOMVO). The same concepts of MVO are used for converging towards the best solutions in a multi-objective search space. For maintaining and improving the coverage of Pareto optimal solutions obtained, however, an archive with an updating mechanism is employed. To test the performance of MOMVO, 80 case studies are employed including 49 unconstrained multi-objective test functions, 10 constrained multi-objective test functions, and 21 engineering design multi-objective problems. The results are compared quantitatively and qualitatively with other algorithms using a variety of performance indicators, which show the merits of this new MOMVO algorithm in solving a wide range of problems with different characteristics.

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“…This strategy has been extensively proved by us as a suitable method of optimizing problems from diverse natures. As a matter of fact, MOOGA has been used to study and improve the reliability of embedded software when diverse hardening techniques are applied 41 , improve Apache server quality metrics when diverse compiler options are used 42,43 , or feature selection for network anomalies 44 . Furthermore, these techniques have been validated by other authors in other areas of knowledge such as integrated engineering or civil engineering [45][46][47][48][49] , production-distribution planning problems 50 , counterrotating compressors 51 , multi-label lazy algorithms 52 , quantitative association rules 53 , design of in-building wireless networks 54 and others [55][56][57][58][59] .…”

Section: Evolutionary Multi-objective Strategy For Tuning a Retina Modelmentioning

confidence: 99%

“…NSGA-II (Non-dominated Sorting Genetic Algorithm II) has been reported to be one of the most successful MOO algorithms 33,42 and is included within of group of elitist selection algorithms that emphasize computational efficiency, such as the Strength Pareto Evolutionary Algorithms SPEA and SPEA2.…”

Section: Evolutionary Multi-objective Strategy For Tuning a Retina Modelmentioning

confidence: 99%

Automatic Tuning of a Retina Model for a Cortical Visual Neuroprosthesis Using a Multi-Objective Optimization Genetic Algorithm

Martínez-Álvarez

Crespo-Cano

Díaz-Tahoces

et al. 2016

Int. J. Neur. Syst.

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The retina is a very complex neural structure, which contains many different types of neurons interconnected with great precision, enabling sophisticated conditioning and coding of the visual information before it is passed via the optic nerve to higher visual centers. The encoding of visual information is one of the basic questions in visual and computational neuroscience and is also of seminal importance in the field of visual prostheses. In this framework, it is essential to have artificial retina systems able to function in a way as similar as possible to the biological retinas. This paper proposes an automatic evolutionary multi-objective strategy based on the NSGA-II algorithm for tuning retina models. Four metrics were adopted for guiding the algorithm in the search of those parameters that best approximate a synthetic retinal model output with real electrophysiological recordings. Results show that this procedure performs well when different trade-offs has to be considered during the design of customized neuro prostheses.

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Tuning compilations by multi-objective optimization: Application to Apache web server

Cited by 10 publications

References 20 publications

Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer’s Disease Therapy

Allostery Inhibition of BACE1 by Psychotic and Meroterpenoid Drugs in Alzheimer’s Disease Therapy

Optimization of problems with multiple objectives using the multi-verse optimization algorithm

Automatic Tuning of a Retina Model for a Cortical Visual Neuroprosthesis Using a Multi-Objective Optimization Genetic Algorithm

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