Documentation

Objective

Given the Holo form of a protein (the complex of a protein structure and its user-specified ligand(s)):

  1. find all unbound forms of that protein (apo-proteins) that lack the specified ligand(s) in the superimposed binding site(s) of the specified ligand(s).
  2. find all other bound forms of that protein (holo-proteins) that include the specified ligand(s)
    3. or other ligands in the superimposed binding site(s) of the specified ligand(s).
  3. align both apo- and holo-proteins to the query holo protein

Given the Apo form of a protein (a protein structure without any ligands):

  1. find all other forms of that protein that bind at least one ligand (holo-proteins).
  2. find all other unbound forms of that protein (apo-proteins) that lack any ligands.
  3. align both apo- and holo-proteins to the query apo protein
Note: ligands are confined to chemical components that are not part of the protein according to the PDB (phosphorylated amino acids can also be considered and specified as ligands). Ligands are named and defined according to their (up to) 3-character code from PDB (i.e. ATP, HEM, ZN).

Methodology

The application is conducting a search within the experimentally determined protein structures in the Protein Data Bank. It retrieves identical proteins with known structures, and then looks whether the specified ligand(s) are present or absent.

Depending on the user’s input, the application can look for the specified ligand(s) in a single specified chain, or the whole protein (all chains). It can find apo-proteins that i) simply lack the specified ligand in a given binding site (but may bind a different ligand at the same site), or ii) lack any known ligand in a given binding site and thus constitute universal apo- sites.