Reply To: Modeling phosphate ion binding site in protein.

[Anonymous]

The ligand docking protocol has been calibrated against binding affinities, although as with most docking protocols, there are rather large error bars. See Jens Meiler and David Baker (2006). “ROSETTALIGAND: Protein-Small Molecule Docking with Full Side-Chain Flexibility” Proteins 65, 538-548. for details. Davis et al. (2009) “Blind docking of pharmaceutically relevant compounds using RosettaLigand.” Protein Sci. 18(9), 1998-2002 is probably also worth looking at.

As Steven said, phosphate is probably going to be a stretch. Compared to the compounds tested in the paper, it’s rather small, so there’s a lot more binding modes that need to be tested (making the search harder), and the interactions are going to be dominated by hydrogen bonding, electrostatics and polar desolvation. Rosetta tends to work best with steric and hydrophobic interactions (i.e. those interactions typically found in protein cores), with electrostatics and polar desolvation being the weak areas.