Nearly every structure-based molecular design endeavor starts with a crystal structure, however, the path from raw PDB files to the input necessary for detailled molecular modelling is not always obvious. In this webinar we will look at a few problems along this path and present novel solutions. We will start with the question of how to efficiently retrieve and align binding sites related to my target of interest. A new method named ASCONA allows to do this on the whole PDB more or less instantaneously. For retrieved structures, hydrogens have to be assigned and oriented including the prediction of the right tautomeric structures including those of the ligand. ProToss is able to address this problem and is fast enough to even re-run it for every scoring calculation. We will also have a look at water molecules and how we can measure their experimental support. In summary, these methods create an ideal starting point for structure-based molecular design and substantially contribute to its success.