In the last years, the importance of water molecules in pose prediction experiments has been widely recognized and several approaches to integrate water molecules into the docking process have been proposed [1,2]. The inclusion of water molecules extends the classical two-body problem of docking a flexible ligand into a protein receptor to a multi-body docking problem as protein-ligand, protein...

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...