Help for Phyre2-ligand

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Phyre2-ligand is a utility to place ligands into pockets (or cavities) in the results from running Phyre2.

When run, Phyre2-ligand will automatically

  • Try to find pockets in the protein model (with the program pyKVFinder), and determine which of those are large enough to contain an organic ligand with at least 5 non-hydrogen atoms.

    • If any pockets are found, the following steps are run:

  • Find any ligands in the PDB entry that corresponds to the Phyre2 template and decide which are large enough to give a reasonable number of docking solutions
  • Examine the UniProt entry corresponding to the PDB entry, and find
    • reactants and products for any reaction the protein is involved in (from the Rhea website)
    • Any cofactors for the protein
    • Any other ligands
    Note that the names and chemical identifiers for the ligands from the PDB and UniProt (or Rhea) may be different for the same compound.
Having performed this analysis, there is a simple 1, 2, 3 for the user to follow to complete the docking.

1 Choose the pocket to dock into (the display in the results pane will update to show the pocket in the protein model)
2 Choose the ligand to dock; in addition to the ligands found for PDB and UniProt, users can enter a ligand of their own choice.

A line drawing of the ligand with a number of synonyms will appear in the bottom right-hand panel
3 Run the docking with AutoDock Vina. The results panel on the left-hand side will be updated with up to 9 different poses found for the ligand in the chosen pocket.

The results can be viewed interactively with JSMol; the poses can be chosen by clicking on the corresponding button; right-clicking (or Ctrl-clicking) the buttons downloads a PDB format file with the protein, the ligand and the cavity coordinates for off-line viewing

Extra help on individual parts of the process can be accessed through tooltips on the Phyre2-ligand results pages by placing the cursor over the Info Icon icons.

Feel free to contact us with problems or comments via e-mail at phyre2@imperial.ac.uk