Virtual Screening Protocol on BlueGene (IGF-IR system)
For this document, virtual screening protocol will be described in detail for IGF-IR system (by Yulin Huang).
1. Identify the target
This is the very fist step for virtual screening. Usually, a single or multiple proteins are selected as targets if their mutations or overexpression are implicated in certain diseases. However, disease relevance alone is not sufficient for target identification. Moreover, the target must be druggable which means the target should be predicted to bind to a drug with high affinity and this binding will bring therapeutic benefit to the patients. The target is defined as druggable if there are drugs already identified for it. Otherwise, druggability can be predicted using evolution rules, structural properties or other destructors.
2. Prepare the target
At this step, you need to prepare the protein structure used for virtual screening. The structures can be downloaded from PDB database if they are available. Make sure which form of the structures Or the structures can be obtained from homology modeling or molecular dynamic simulations. Monoatomic ions should be carefully treated and usually they are treated as part of the receptor if they were within ca. 10Å from the binding site. In terms of water molecules, prior knowledge is needed for decisions. If the system is known to have water-mediated interactions (i.e, ErbB family receptors), then the waters should be included as part of the receptors. If not, waters should be removed. For histidine residues, they are treated based on the environment, i.e., which nitrogen was coordinated with ions and/or ligands. Finally, all the protein structures are aligned to a common frame (added hydrogen and minimize the H).
3. Database Preparation
4. Run Docking on Bluegene
(1) Make the grid for the protein.
cat <<EOF >box.in yes $box_margin ./selected_spheres.sph 1 box.pdb EOF
cat <<EOF >grid.in
compute_grids yes
grid_spacing $grid_spacing
output_molecule yes
contact_score no
chemical_score no
energy_score yes
energy_cutoff_distance 999
atom_model a
attractive_exponent ${attractive}
repulsive_exponent ${repulsive}
distance_dielectric yes
dielectric_factor 4
bump_filter yes
bump_overlap 0.75
receptor_file ./receptor.mol2
box_file ./box.pdb
vdw_definition_file ./vdw.defn
chemical_definition_file ./chem.defn
score_grid_prefix ./${system}.rec
receptor_out_file ./${system}.rec.grid.mol2
EOF
Among them, the parameters are set as follows: set grid_spacing = 0.3 set attractive = 6 set repulsive = 9 set box_margin = 8</nowiki>
(2) Dock to the subset of the database
