of steepest descent, conjugate gradient, and truncated Newton
methods using 0.01 A ̊ RMSD for convergence criteria) [15]
(seeNote 4).- The obtained structure (Fig.1a) is used by a GRID run with
default parameters for the water oxygen probe [16] to generate
a grid corresponding to this probe (Fig.1b).
Fig. 1Example of the Method I pipeline used to de novo predict positions of water molecules on the surface of
the protein receptor prior to docking a GAG molecule: the complex of 3-O-sulfotransferase-3 and heparin
tetrasaccharide (PDB ID 1T8U, 1.95 A ̊). (a) Minimized protein receptor structure (in stick representation); (b)
Isosurfaces confining the volumes corresponding to favorable potential energies for water oxygen atomic
probe calculated by GRID (in yellow, in wireframe representation); (c,d) Water molecules (oxygen atoms)
placed into the grid points corresponding to the energy minima for water molecular probe (in red, in ball
representation) with and without the corresponding isosurfaces, respectively. (e) Isosurfaces confining the
volumes corresponding to favorable potential energies for water exclusion sp3-carbone atomic probe
calculated by GRID (in white, in wireframe representation); (f) Overlap of the exclusion probe isosurfaces
with the experimentally obtained structure of the bound ligand (in thick sticks colored by element)
Solvent Inclusion in Docking Glycosaminoglycans 447