AMIDE v2: High-Throughput Screening Based on AutoDock-GPU and Improved Workflow Leading to Better Performance and Reliability.

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. AMIDE stands for AutoMated Inverse Docking Engine. It was initially developed in 2014 to perform inverse docking on High Performance Computing. AMIDE version 2 brings substantial speed-up improvement by using AutoDock-GPU and by pulling a total revision of programming workflow, leading to better performances, easier use, bug corrections, parallelization improvements and PC/HPC compatibility. In addition to inverse docking, AMIDE is now an optimized tool capable of high throughput inverse screening. For instance, AMIDE version 2 allows acceleration of the docking up to 12.4 times for 100 runs of AutoDock compared to version 1, without significant changes in docking poses. The reverse docking of a ligand on 87 proteins takes only 23 min on 1 GPU (Graphics Processing 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 of GPUs used, allowing a significant reduction of the duration of the inverse docking process on large datasets.

A simplified method to evaluate the loss of domain.

PURPOSE: The treatment of giant incisional hernia (IH) with loss of domain (LOD, IHLD) is considerably challenging due to technical difficulties and subsequent post-operative complications. These post-operative risks may be anticipated by calculating the abdominal cavity (AC) volume (ACV) and the IH volume (IHV) on the preoperative CT-scans, using the AC and IH dimensions (Tanaka's method) or using tridimensional volumetry (Sabbagh's method). These techniques are often time-consuming and require specific softwares. The aim of the present study was to develop a simple method to rapidly obtain the LOD-ratio on the preoperative CT-Scan. METHODS: The CT-scans (n = 89) of patients with IHLD were retrospectively studied. Several ratios were calculated using different parameters of the AC and the IH, including width, height and depth, the areas (axial and sagittal ellipse, as well as freehand sagittal surface areas) and these were compared with the reference methods of Sabbagh et al. and Tanaka et al. RESULTS: The LOD ratios calculated from the two reference methods gave similar results (ICC = 0.82, p < 0.0001). The new "R-ratios" (Reims-ratios) obtained from the IH and AC surface areas measured using the "freehand ROI" tool on sagittal view or roughly evaluated by an ellipse on axial view showed excellent correlation with both reference ratios (all ICC ≥ 0.71, p < 0.0001). CONCLUSION: The LOD ratio may be quickly obtained by drawing two circles on the pre-operative CT scan ("R ratios") and available on the webpage https://romeo.univ-reims.fr/Rratio/ . This will certainly help surgeons to routinely anticipate the post-operative complications before IHLD repair.