Receptor flexibility is a critical issue in structure-based virtual screening methods. Although a multiple-receptor conformation docking is an efficient way to account for receptor flexibility, it is still too slow for large molecular libraries. It was reported that a fast ligand-centric, shape-based virtual screening was more consistent for hit enrichment than a typical single-receptor conform...

We present a reliable and accurate solution to the induced fit docking problem for protein–ligand binding by combining ligand-based pharmacophore docking, rigid receptor protein structure prediction with explicit solvent molecular dynamics simulations. This novel methodology in detailed retrospective prospective testing succeeded determine modes root-mean-square deviation within 2.5 Å over 90% ...

We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in an...

We consider the optimization of cross-docking operations at three INtermodal LOgistics Platforms (INLOPs) a large European car manufacturer (ECM). The planning horizon is week and time bucket day. An inbound flow products gradually received over by truck from inland suppliers, has to be loaded into containers which are then shipped offshore production plants. full content container must availab...

This study addresses the pickup and delivery problem for cross-docking strategy, in which shipments are allowed to be transferred from suppliers to retailers directly as well as through cross-docks. Usual models that investigate vehicle routing in cross-docking networks force all vehicles to stop at the cross-dock even if a shipment is about to a full truckload or the vehicle collects and deliv...

Today, many companies after achieving improvements in manufacturing operations are focused on the improvement of distribution systems and have long been a strong tendency to optimize the distribution network in order to reduce logistics costs that the debate has become challenging. Improve the flow of materials, an activity considered essential to increase customer satisfaction. In this study, ...