Glide WS Visualizer Panel
Visualize Glide WS scoring terms in the Workspace, showing the parts of the structure that contribute to the score.
To open this panel, you can:
- Click the Workflow Action Menu
for the entry group and choose Glide WS Visualizer. - Click the Tasks button and browse to Receptor-Based Virtual Screening → Glide WS Visualizer.
All entries in the group that have Glide WS data are selected and loaded into the panel, and the first entry that has Glide WS data is visualized.
- Features
- Additional Resources
Glide WS Visualizer Panel Features
- Set Up button
- Previous and Next buttons
- Receptor and ligand titles
- Total Glide WS text
- Table
- List of Glide WS Terms
- WaterMap sites option
- Tips
- Set Up button
-
Set up the visualization for the selected entry group. You can use this feature to select a different entry group, or select a subset of entries, and set up the visualization. Clicking the WS button in a new entry group also sets up the visualization for an entire group.
- Previous and Next buttons
-
Click these buttons to step through the selected ligands in the project entry group. The next or previous selected ligand is loaded for visualization and the viewer is updated with the data for the new ligand. You can also use the left and right arrow keys.
- Receptor and ligand titles
-
These text fields report the title of the receptor and the title of the ligand that were used for the visualization.
- Total Glide WS text
-
This text shows the total Glide WS value for the ligand.
- Table
-
The table lists the Glide WS terms with values and descriptions. Not every term has a visualization, but all terms are listed. A term can be visualized by selecting its row in the table.
Visualization icon Rows that have a visualization are marked with an eye icon at the left of the row. If there are multiple rows for a particular term that have visualizations, the parent row has the icon when the rows are hidden. Glide WS Term Names of the Glide WS terms that appear in the GUI as well as in props.py. A list of terms and their definitions can be found in the table below. Score Value of the Glide WS term for the particular instance of the term. Information icon A description of the Glide WS term is displayed as a tooltip when you pause the pointer over the icon. - List of Glide WS Terms
-
The following is a list of Glide WS terms and their definitions that appear in the GUI as well as in props.py:
Lipophilic Interaction between lipophilic atoms, driven by hydrophobic effect Void Reward Reward for ligand halogen in large protein void Sitemap Score Phobic sitemap term Phobically Enclosed Hydrogen Bond Reward for hydrophobically enclosed hydrogen bond Van der Waals Van der Waals energy Electrostatic Environment Reward Electrostatic reward Water Displacement Reward Methyl reward Hydrophobic Void Reward Reward for CH2/halogen in small hydrophic void Pi-Cation Pi-Cation reward Mass Adjustment for Rotatable Bonds Entropy correction for rotatable bonds Neutral Hydrogen Bond Hydrogen bond score Hydroxyl Interaction Hydrogen bond score for ligand hydroxlys Enclosed Hydrogen Bond Enclosed hydrogen bond reward for a pair of hydrogen bonds Solvation Adjustment Hydrogen bond reduction of solvated hydrogen bonds Electrostatic Adjustment Cancels a geometrically weakly-formed special pair reward Methyl-Aromatic Interaction Intra-ligand CH3-aromatic phobic packing reward Charged Ligand Motif Reward for ligand binding to three proximal sidechains binding to a common water Polar Clash Polar clash between ligand and protein atom Intra-ligand Polar Clash Polar clash intra-ligand Protein Desolvation Penalty Penalty for desolvation of a triad of proximal sidechains binding to a common water Tetrahedral Water Desolvation Penalty for removal of a tetrahedrally hydrogen bound water Ligand Desolvation Penalty Ligand amide and carbonyl desolvation penalty Burial of Ring Donor Aromatic O and N desolvation penalty Protein Backbone Desolvation Protein carbonyl desolvation penalty Protein Sidechain Desolvation Tyrosine hydroxyl H penalty Aromatic-ARG Stacking Reward Reward for ligand aromatic ring stacked on ARG sidechain face Congested Water Penalty Penalty for removal of water binding to two protein oppositely directed carbonyl and not compensated by ligand Protein Backbone Desolvation Backbone desolvation penalty Van der Waals Adjustment Penalty for low Evdw relative to ligand size Charged Sidechain Desolvation Charged sidechain desolvation penalty ARG Desolvation Penalty Penalty for ligand moving water from ARG sidechain amide NH-Water-NH Desolvation Penalty Penalty if water bound to hydroxyl amide of same residue is removed and not compensated by ligand Protein Backbone Desolvation Backbone amide desolvation Bridging Water Displacement Penalty for removal of water bridging oppositely charged sidechains without ligand desolvation Bridging Water Displacement Desolvation of bridging water penalty Bridging Water Displacement Penalty for removing a water coordinated to three sidechains two are ASP/GLU Pair of Phobically Enclosed Hydrogen Bonds Hydrophobically enclosed hydrogen bond pair involving ligand hydroxyl Ligand H-Bond Donor Clash Penalty for two bound ligand donors that are too close together Phobic Enclosure Score Ligand phobic enclosure score Ligand Ring Adjustment Reduction of lipophilic score for solvent exposed ligand regions Sitemap Polar Grid Polar clash penalty Ligand Electrostatic Adjustment Reward for multiple hydrogen bonds to ligand sulfonamide Ligand Donor Desolvation Penalty for removing waters coordinated to a proximal series of amide donors Pair Ligand Desolvation Penalty for intra-ligand charge-charge clash Negative Ligand Multiple Hydrogen Bond Reward for placing positive ligand charge at location of water that was multiply bound to series of amide backbone donors Halogen Water Displacement Reward for placing ligand halogen on face of protein PHE ring Twisted Amide Penalty for unusual ligand bond angles Recessed Salt Bridge Reward for ligand binding a positive charge to recessed ASP/GLU sidechain Ligand Internal Energy Internal ligand-ligand clash penalty Axial Adjustment Ligand axial group off ring clashing with ligand penalty Protein Ligand Clash Penalty for ligand atom being too close to protein Aromatic Torsion Strain Aromatic Torsion Strain value Receptor Offset Equivalent to zscore, is receptor offset from core-packing Ligand State Penalty Ligand state penalty value - Show options
-
Specify features to show in the Workspace as part of the visualization.
- WaterMap stes option
-
Show WaterMap sites in the Workspace. The selected visualizations are hidden and the WaterMap spheres are added to the Workspace for the receptor for sites within 5Å of the ligand, with sphere color and radius adjusted according to the site's entropy and potential energy values. The WaterMap sites are hidden (and the option deselected) if you select a visualization in the table or choose a different receptor.
- Tips
-
This text provides some suggestions for using the panel.