… of water molecules on the accuracy of ligand−protein docking simulations by expanding the
number of ligand−protein … test set 93 that contain water molecules in their crystal structures. …

… dealing with key water molecules in protein−ligand docking and its implementation in the
protein−ligand docking program GOLD. The method represents each water molecule by an all-…

… should be rewarded by the scoring function because a displaced water molecule gains …
water molecules in protein−ligand docking and its implementation in the protein−ligand docking …

… water molecules, protein flexibility, covalent ligands, treatment of target macromolecules
different from proteins, … deals with the explicit treatment of structural water molecules in docking. …

… We perform the docking, starting from protein chains that are solvated in explicit shells of
water molecules. Once the proteins have formed a 3D encounter complex, removal of …

… new protein–protein docking algorithm. In this work, we are testing HINT scoring and water
… While we believe that protein–protein docking algorithms should account for physical effects …

… In fact, we observe a substantial variation in the final number of water molecules in the
docked structures for the complexes that we used to test our protocol (see below, Table 4). …

… protein-ligand complexes. In this paper, we focus on the influence of water molecules on the
structure of protein… the placement of single water molecules in the docking algorithm of FlexX…

… docking with the variable numbers of the water molecules was also efficient. Above all, the
multi-body docking … the water molecules that explicitly participating in protein-ligand binding. …

… RosettaLigand to perform protein-ligand docking with flexible water molecules, and taking …
the interfacial water molecules explicitly into consideration in the protein-ligand docking, and …