Reply To: Modeling phosphate ion binding site in protein.

[Anonymous]

The ligand docking application is somewhat pocket-based. You specify one or more potential starting locations (pockets) and then the ligand docking application explores various binding poses in the region of that pocket. From the flags you give, it’s set up to search a 5 Angstrom sphere (-uniform_trans) with a random rotational orientation (-randomize2) around the -start_from location. It won’t look at possible binding sites outside of that 5 Ang sphere. To search other sites, add them with additional -start_from lines. Especially with something like phosphate, you’ll need to narrow down the potential binding sites in order to get decent results. To do this I’d suggest examining the starting structure, and applying some chemical intuition about where the ligand might bind.

Note that having the top 5% all being in the same location doesn’t necessarily mean that you’re getting poor sampling – it just might be that there’s a very tight binding funnel and that spot is the best binding location. You can tell the difference by looking at some of the higher energy structures.

To that end, you do need to have R installed in order to use the plot_funnels.R application. If installing R is an issue for you, note that you can create similar plots with other graphing programs, by plotting the “interface_delta” values against the “ligand_auto_rms_no_super” values in the output score file.