After performing a search for a specific PDB id and chain in Search for PDBs Section, the resulting ids, as well as the query parameters, are provided in Search for ligand groups Section. In this Section, users can set three parameters before searching for ligands and also, they can provide an email to be informed about results, as, depending on the size of the PDB id list, the ligand search can take a while.

By clicking on More options, users are able to set three additional parameters.

Cutoff distance (Ångström): maximum distance threshold to find neighbors ligands. Two ligands are neighbors if two of their atoms are distant from each other by at most the chosen cutoff.

Minimum number of atoms: minimum number of heavy atoms to consider a molecule as a ligand and not an artifact.

Set of Artifacts of Crystallography: list of molecules that should be considered as crystallography artifacts and not real ligand.

nAPOLI can detect ligands considered artifacts according to the parameters Minimum number of atoms and Set of Artifacts of Crystallography. After detecting likely artifacts with these parameters, users could decide if they will ignore and delete these ligands from their data set. Ignored artifacts will not be used in the protein-ligand interactions analysis.

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

After processing the query, the section Search for ligand groups provides a new page, with the resulting PDB ids and its respective chains and ligands. There are the following panels:

PDBs search: shows the parameters for the query performed in the Section Search for PDBs.

List of retrieved PDBs: provides the list of PDB ids that are similar to the PDB id and chain entered in the query performed in Section Search for PDBs.

Groups search: parameters informed in Section More options concerning ligands.

PDBs without valid ligands: PDB ids which do not have valid ligands. We consider valid ligands those ones that are not ions.

Found ions: shows PDB id, chain, ion and position in which an ion was found in PDB file format (Atom serial number field). Note that nAPOLI do not consider ions in interaction calculation.

Some statistics: a table with the PDB id and chain and the number of ligands for each chain. Also there is a table with the number of ligands for each chain id (letter).

Found ligands: this panel lists all PDB entries and ligands similar to the PDB id and chain submitted as query, as well as their values for Residue sequence number field in the PDB file format. The Residue sequence number is provided to differentiate cases in which the same ligand appear more than once in the same PDB id and chain. For instance, 2AAI:B:NAG:281 and 2AAI:B:NAG:271, which are two NAG molecules.
The ligands are grouped in the list in accordance with the pocket of the protein with which they interact. The user must select a group of ligands by clicking on its respective radio button to proceed by clicking on the button Go, run nAPOLI. Also, ligands are shown in green, while artifacts are shown in gray. There is a blue button, called Remove all artifacts of crystallography, which removes all crystallographic artifacts.
The user can remove a ligand by clicking on the x on the right hand side of the ligand name. All ligands (even the excluded ones) can be restored by clicking on the green button called Restore all removed items.

Current email to contact: the email address provided to be informed that the query submitted in Search for ligand groups is shown in this panel. Also, users can change this email address.

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.