How should ligands be prepared?
It is possible to prepare ligands in an external program. If the ligands are saved in a molecular data format capable of storing the various properties (such as charge and bond order), Molegro Virtual Docker will be able to read them. However, it is not necessary to do so. Molegro Virtual Docker is able to determine atom connectivity, assign bond orders, hybridization, add explicit hydrogens, and assign charges automatically. It is also possible subsequently to modify the various properties in the GUI. Molegro Virtual Docker can read ligands stored in the following formats: • Protein Data Bank format (*.pdb *.ent) • Sybyl Mol2 format (*.mol2) • MDL Mol format (*.mol *.sdf *.sd *.mdl) • Molegro MVDML format (*.mvdml) • How should proteins be prepared? As with ligands, proteins can be prepared in an external program. However, it is not necessary to do so. Molegro Virtual Docker will perform a residue based template matching on the protein and assign the necessary molecular properties. Di
