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What is target preparation and why is it important?

Many experimentally determined structures of targets (e.g., proteins, DNA, RNA) are commonly available from sources such as the PDB. However, many of these experimentally determined structures lack much of the information needed to carry out a rigorous, all-atom simulation of target-ligand interactions. To correct common structural problems, target preparation begins by taking in an experimentally determined target structure and outputting a low energy, all-atom structure.

To perform target preparation in Maestro, choose Workflows → Protein Preparation Wizard.

The Protein Preparation Wizard allows you to add missing hydrogen atoms, build in missing residues and loops, identify overlapping atoms, automatically assign missing bond orders, calculate ligand protonation states, and optimize the hydrogen-bonding network. Explicit water molecules from a crystal structure can be removed, or if necessarily retained, their orientations can be automatically optimized. Common crystallographic errors can also be identified and corrected.

Click the Help button in the Protein Preparation Wizard panel for more detailed information.

Keywords: target preparation, protein preparation, docking, experimental structure

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