Pockets

You can create Pocket molecules, which represent binding sites on macromolecules. These can be used to view hydrogen bonds, perform molecular docking, and pharmacophore analysis.

You can save and load pockets as SDF or Mol2 files using the same save and load system used for small molecules. We insert a metadata flag, is_pocket, which indicates to Molchanica to load these as pockets. Once loaded, surface meshes and areas of exclusion are generated automatically, as a derivative of atom and bond data.

These can be manipulated, selected, and closed in a way similar to other molecule types. They can be loaded into the molecule editor using the sidebar, and combined with a ligand for use in pharmacophores. When saving a ligand with this association, it will be saved and loaded with the ligand. See the Pharmacophore section for more information.