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In this paper, we propose a two-stage algorithm for biomolecular docking sites selection problem. The proposed method can be easily parallelized in the cloud computing frame work. Given the ligand/receptor docking pair, the algorithm is especially suitable when the ligand size is comparatively much smaller than the receptor. The propsed Probe-dig algorithm first survey the surface of the receptor and evaluate the potentials of these possible candidate locations on the receptor before proceed to further reexamine docking sites with finer grains inquisition in performing the later AutoDock examinations.
The method is implemented upon the widely employed automated molecular docking simulation software package, AutoDock. Experiments are set up to test upon Japanese encephalitis related biomolecules in virology research. In average, the proposed Probe-dig algorithm is about 1.3 folds faster in LE=−3.40 in this experiments. Hadoop MapReduce frameworks are used in our experiments to parallelize the underlying massive computation works corresponding to ligand-receptor pairs examined under the experiment.
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