In this Section, users can submit their own PDB files and provide an already known list of PDBs, its chains and ligands to be analyzed. They also can provide an email to be informed about results, as, depending on the size of the list, the Protein-ligand interactions processing can take a while.

Choose your PDB files: in this panel, users can select their PDB files of interest.

Insert your PDB entries: in this panel, users can provide their PDB entries of interest. In this list, each entry should be separated by a Space and should be in the following format: PDB-ID or filename:CHAIN:LIGAND-NAME:LIGAND-NUMBER. The PDB id or filename should be a valid filename; the Chain should be 1 character in length; the Ligand name should be 1-3 characters in length; and the Ligand number should be a valid integer.

Choose a template to the Structural alignment: users can provide a PDB id and a chain to be used as template to the Structural alignment that is performed by nAPOLI.

Email to contact: users can provide an email to be informed that the submitted query was processed.

Configure nAPOLI parameters: users can set the distance criteria for each type of interaction in this panel. Distance minimum and maximum thresholds can be set by dragging the interaction type respective slider or by typing on respective minimum and maximum text boxes.