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  • Title: A new Lamarckian genetic algorithm for flexible ligand-receptor docking.
    Author: Fuhrmann J, Rurainski A, Lenhof HP, Neumann D.
    Journal: J Comput Chem; 2010 Jul 15; 31(9):1911-8. PubMed ID: 20082382.
    Abstract:
    We present a Lamarckian genetic algorithm (LGA) variant for flexible ligand-receptor docking which allows to handle a large number of degrees of freedom. Our hybrid method combines a multi-deme LGA with a recently published gradient-based method for local optimization of molecular complexes. We compared the performance of our new hybrid method to two non gradient-based search heuristics on the Astex diverse set for flexible ligand-receptor docking. Our results show that the novel approach is clearly superior to other LGAs employing a stochastic optimization method. The new algorithm features a shorter run time and gives substantially better results, especially with increasing complexity of the ligands. Thus, it may be used to dock ligands with many rotatable bonds with high efficiency.
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