In order to help you to analyze the Protein-ligand interactions, there are three functionalities available in nAPOLI:

  • In the Insert nAPOLI entries section, users can provide an already known list of PDB ids, its chains and ligands to be analyzed. Then, nAPOLI will compute all Protein-ligand interactions to the chosen data set.

  • In the Upload PDB files section, users can submit their own PDB files and provide an already known list of PDB ids, its chains and ligands to be analyzed. Then, nAPOLI will compute all Protein-ligand interactions to the chosen data set.

  • In the Compose a new data set section, users start providing a PDB id and its chain to search for chains with similar sequence in the PDB. Following, nAPOLI aligns all structures and search for groups of ligands located at the same region. All detected regions containing ligands will be returned to the user who, accordingly, can select and submit to nAPOLI a group of ligands to be analyzed. Then, nAPOLI will compute all Protein-ligand interactions to the chosen data set.

    This functionality is useful when the user has a protein of interest and, in an exploratory way, the user can compose a new data set consisting of ligands located at the same region.