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                <term xml:lang="en">Toxoplasma gondii</term>
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              <p>Molecular docking is widely used in computed drug discovery and biological target identification,but getting fast results can be tedious and often requires supercomputing solutions. AMIDEstands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inversedocking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvementby using AutoDock-GPU and by pulling a total revision of programming workflow, leadingto better performances, easier use, bug corrections, parallelization improvements and PC/HPCcompatibility. In addition to inverse docking, AMIDE is now an optimized tool capable of highthroughput inverse screening. For instance, AMIDE version 2 allows acceleration of the dockingup to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes indocking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (GraphicsProcessing Unit), while version 1 required 300 cores to reach the same execution time. Moreover,we have shown an exponential acceleration of the computation time as a function of the number ofGPUs used, allowing a significant reduction of the duration of the inverse docking process on largedatasets.</p>
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