PRO_LIGAND: An approach to de novo molecular design. 3. A genetic algorithm for structure refinement |
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Authors: | David R Westhead David E Clark David Frenkel Jin Li Christopher W Murray Barry Robson Bohdan Waszkowycz |
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Affiliation: | (1) Proteus Molecular Design Ltd., Proteus House, Lyme Green Business Park, SK11 0JL Macclesfield, Cheshire, U.K. |
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Abstract: | Summary Recently, the development of computer programs which permit the de novo design of molecular structures satisfying a set of steric and chemical constraints has become a burgeoning area of research and many operational systems have been reported in the literature. Experience with PRO_LIGAND—the de novo design methodology embodied in our in-house molecular design and simulation system PRO-METHEUS—has suggested that the addition of a genetic algorithm (GA) structure refinement procedure can add value to an already useful tool. Starting with the set of designed molecules as an initial population, the GA can combine features from both high- and low-scoring structures and, over a number of generations, produce individuals of better score than any of the starting structures. This paper describes how we have implemented such a procedure and demonstrates its efficacy in improving two sets of molecules generated by different de novo design projects. |
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Keywords: | Drug design De novo design Genetic algorithms |
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