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Parallel multi-objective algorithms for the molecular docking problem [article]

Jean-Charles Boisson, Laetitia Jourdan, El-Ghazali Talbi
2008 arXiv   pre-print
Molecular docking is an essential tool for drug design.  ...  This model has been validated with two multi-objective genetic algorithms on instances from the literature dedicated to the docking benchmarking.  ...  NEW MODEL FOR THE MOLECULAR DOCKING PROBLEM A. Existing multi-objective models Most of the docking methods use a mono-objective modeling.  ... 
arXiv:0811.0514v1 fatcat:whvlvyzgw5hfzcgko2a44bekli

Parallel multi-objective algorithms for the molecular docking problem

Jean-Charles Boisson, Laetitia Jourdan, El-Ghazali Talbi, Dragos Horvath
2008 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology  
This model has been validated with two multi-objective genetic algorithms on instances from the literature dedicated to the docking benchmarking.  ...  Molecular docking is an essential tool for drug design.  ...  NEW MODEL FOR THE MOLECULAR DOCKING PROBLEM A. Existing multi-objective models Most of the docking methods use a mono-objective modeling.  ... 
doi:10.1109/cibcb.2008.4675777 dblp:conf/cibcb/BoissonJTH08 fatcat:cguqvlkpszak3gjgakpx4jkfle

A New Multi-objective Approach for Molecular Docking Based on RMSD and Binding Energy [chapter]

Esteban López-Camacho, María Jesús García-Godoy, José García-Nieto, Antonio J. Nebro, José F. Aldana-Montes
2016 Lecture Notes in Computer Science  
Molecular docking problems are traditionally tackled with single-objective, as well as with multi-objective approaches, to minimize the binding energy.  ...  In addition, a comparison with LGA, a reference single-objective evolutionary algorithm for molecular docking (AutoDock) is carried out.  ...  The problem: Multi-Objective Docking A multi-objective optimization problem is characterized by two spaces: the decision and the objective spaces.  ... 
doi:10.1007/978-3-319-38827-4_6 fatcat:o22umjcskffqta3tls56olicfy

Solving Molecular Docking Problems with Multi-Objective Metaheuristics

María García-Godoy, Esteban López-Camacho, José García-Nieto, Antonio Nebro, José Aldana-Montes
2015 Molecules  
In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems.  ...  Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy  ...  Author Contributions María Jesús García-Godoy selected the objectives to be optimized in the energy function, prepared the benchmark to be used, analyzed the results obtained and designed the experiments  ... 
doi:10.3390/molecules200610154 pmid:26042856 fatcat:h5llsmx7unecpdhqtucew5tb7i

Multi-objective optimization methods in drug design

Christos A. Nicolaou, Nathan Brown
2013 Drug Discovery Today : Technologies  
Drug discovery is a challenging multi-objective problem where numerous pharmaceutically important objectives need to be adequately satisfied for a solution to be found.  ...  This paper reviews the latest multi-objective methods and applications reported in the literature, specifically in quantitative structureactivity modeling, docking, de novo design and library design.  ...  Acknowledgements CN would like to thank Christine Humblet (Eli Lilly & Co.) for reviewing the manuscript and providing useful feedback. NB is funded by Cancer Research UK Grant no. C309/A8274.  ... 
doi:10.1016/j.ddtec.2013.02.001 pmid:24050140 fatcat:tkaroywsf5dfhmwh7sbi7quoju

Parallel Genetic Algorithm with Biased Initial Population for the Simultaneous Hybrid Modeling of Molecular Assemblies

M Rusu, S Birmanns
2010 Microscopy and Microanalysis  
MOSAEC (Multi-Object Simultaneous Alignment using Evolutionary Computing) is a population-based technique derived from genetic algorithms and enhanced with tabu-search strategies to prevent the unnecessary  ...  For example, an atomic interpretation of low-resolution cryo-electron microscopy (cryo-EM) maps can be achieved by docking each component into the envelope of the entire assembly.  ...  MOSAEC (Multi-Object Simultaneous Alignment using Evolutionary Computing) is a population-based technique derived from genetic algorithms and enhanced with tabu-search strategies to prevent the unnecessary  ... 
doi:10.1017/s1431927610057429 fatcat:hdvjkoapkrcfxfnddmlqinu6rm

Molecular Optimization Using Computational Multi-Objective Methods

C.A. Nicolaou, N. Brown, C.S. Pattichis
2007 Zenodo  
Multi-objective optimization (MOOP) methods introduce a new approach for gaining optimality based on compromises and trade-offs among the various objectives.  ...  Implicitly, SOOP-based methods assume that the optimal solution for an objective will also be the optimum for any other objectives involved in the profiling of a molecule.  ...  multi-objective, as demonstrated by the possibility of a compound set to exhibit several nearly EA evolutionary algorithm, GA genetic algorithm, GALAHAD Genetic Algorithm with Linear Assigment for the  ... 
doi:10.5281/zenodo.2555799 fatcat:r4d75kodwjatppw2z4yohbdsva

A BRIEF SURVEY ON BIO INSPIRED OPTIMIZATION ALGORITHMS FOR MOLECULAR DOCKING [article]

Mayukh Mukhopadhyay
2014 bioRxiv   pre-print
Mathematically, molecular docking can be formulated as an optimization problem in which the objective is to minimize the intermolecular bound conformational energy of two interacting molecules.  ...  In this brief survey, after a concise introduction on nature inspired computing, the application of bio inspired optimization algorithms in molecular docking has been studied.  ...  The author is grateful to Dr Parama Bhaumik, for guidance and valuable technical inputs.  ... 
doi:10.1101/006833 fatcat:tcqw7um3rrhepkibowbqcqejpe

An effective docking strategy for virtual screening based on multi-objective optimization algorithm

Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang
2009 BMC Bioinformatics  
Results: In this paper, two multi-objective optimization methods, called MOSFOM, were developed for virtual screening, which simultaneously consider both the energy score and the contact score.  ...  Conclusion: The multi-objective optimization method was successfully applied in virtual screening with two different scoring functions that can yield reasonable binding poses and can furthermore, be ranked  ...  Rolf Hilgenfeld for careful reading this manuscript, and the referees for helpful suggestions and comments. This work was supported by the  ... 
doi:10.1186/1471-2105-10-58 pmid:19210777 pmcid:PMC2753843 fatcat:of3nk46keff6zfo64pqqj4cqce

Biskit A software platform for structural bioinformatics

R. Grunberg, M. Nilges, J. Leckner
2007 Bioinformatics  
At the same time, Biskit offers a software platform for the rapid integration of external programs and new algorithms into complex structural bioinformatics workflows.  ...  Moreover, Biskit simplifies the parallelization of time consuming calculations via PVM (Parallel Virtual Machine).  ...  We thank Wolfgang Rieping, Michael Habeck, Olivier Perrin and David Giganti for discussions and code contributions.  ... 
doi:10.1093/bioinformatics/btl655 pmid:17237072 fatcat:dldrreathbatrapoueyulsfj3u

Strategies of multi-objective optimization in drug discovery and development

Orazio Nicolotti, Ilenia Giangreco, Antonellina Introcaso, Francesco Leonetti, Angela Stefanachi, Angelo Carotti
2011 Expert Opinion on Drug Discovery  
Drug discovery and development is a typical multi-objective problem and its successes or failures depend on the simultaneous control of numerous, often conflicting, molecular and pharmacological properties  ...  Therefore, multi-objective optimization methods, which have recently been introduced to the field of molecular discovery, represent the ultimate frontier in chemoinformatics.  ...  The authors state no conflict of interest and have received no payment in preparation of this manuscript.  ... 
doi:10.1517/17460441.2011.588696 pmid:22646211 fatcat:enutgmi3s5hbdeiy4rg7gfymce

Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates [article]

Tim Cofala, Lars Elend, Philip Mirbach, Jonas Prellberg, Thomas Teusch, Oliver Kramer
2020 arXiv   pre-print
We propose an evolutionary multi-objective algorithm (EMOA) to design potential protease inhibitors for SARS-CoV-2's main protease.  ...  Based on the SELFIES representation the EMOA maximizes the binding of candidate ligands to the protein using the docking tool QuickVina 2, while at the same time taking into account further objectives  ...  Acknowledgements We would like to thank Ahmad Reza Mehdipour, Max Planck Institute of Biophysics, Frankfurt, Germany, for useful suggestions and comments that helped to improve this manuscript.  ... 
arXiv:2005.02666v2 fatcat:s3qcqj7klbgzlps2gxcu6zhyke

Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions

Mirabela Rusu, Stefan Birmanns
2010 Journal of Structural Biology  
Here we introduce a novel method based on genetic algorithms, for the effcient exploration of the multi-body registration search space.  ...  The algorithm was implemented using the Sculptor molecular modeling framework, which also provides a user-friendly graphical interface and enables an instantaneous, visual exploration of intermediate solutions  ...  Acknowledgments We thank Willy Wriggers for stimulating discussions and valuable advice regarding the project, Teresa Ruiz and Michael Radermacher for helpful comments and Manuel Wahle for kind input.  ... 
doi:10.1016/j.jsb.2009.12.028 pmid:20056148 pmcid:PMC2872094 fatcat:3agk453uibeoxnbo26f57r3s7u

Supercomputer Docking

2019 Supercomputing Frontiers and Innovations  
Thus, the docking problem turns into the global optimization problem.  ...  The "Faster, even faster" mantra long time was the main goal of docking algorithms and some of popular docking programs can dock one ligand at one processor for less than 1 minute even less, e.g. the ICM  ...  The research is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University, including the Lomonosov supercomputer [100] .  ... 
doi:10.14529/jsfi190302 fatcat:fabevvn3xna6fkoiywitnlx25m

Metaheuristics Based Optimization Technique for Protein-Ligand Docking

2019 International journal of recent technology and engineering  
The approach carries out docking and computations of molecular interactions required for SF in parallel so that the time efficiency is improved.  ...  In this paper we present a novel approach for molecular docking which is based on parameterized and parallel metaheuristics which is useful in leveraging heterogeneous computing based on heterogeneous  ...  Molecular docking technique docks small molecules to the macromolecular targets.  ... 
doi:10.35940/ijrte.c6834.098319 fatcat:lkpdr24mnvffpdaanqjwfvvzhy
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