MoDock: A multi-objective strategy improves the accuracy for molecular docking
نویسندگان
چکیده
منابع مشابه
Solving molecular docking problems with multi-objective metaheuristics.
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. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarif...
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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-object...
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Ligand-protein docking is an optimization problem based on predicting the position of a ligand with the lowest binding energy in the active site of the receptor. Molecular docking problems are traditionally tackled with single-objective, as well as with multi-objective approaches, to minimize the binding energy. In this paper, we propose a novel multi-objective formulation that considers: the R...
متن کاملMolDock: a new technique for high-accuracy molecular docking.
In this article we introduce a molecular docking algorithm called MolDock. MolDock is based on a new heuristic search algorithm that combines differential evolution with a cavity prediction algorithm. The docking scoring function of MolDock is an extension of the piecewise linear potential (PLP) including new hydrogen bonding and electrostatic terms. To further improve docking accuracy, a re-ra...
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In this study, a cross-docking system is designed at strategic and tactical levels. For making the strategic decisions, a multi-objective nonlinear location allocation model for cross-docks is presented based on a distri-bution location allocation model by Andreas Klose and Andreas Drexl. The model is further developed to in-clude the whole supply chain members and the objective functions are w...
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ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2015
ISSN: 1748-7188
DOI: 10.1186/s13015-015-0034-8