Error. You are trying to view too many points. Reduce one of the slider ranges.
Pharmacophoric changes:
1
6
Activity change:
0
4
Fit to activity and inactivity points
Error. What you have entered is neither a valid pdb code nor a valid smiles string.
Welcome to the Tutorial for OOMMPPAA.
Below is the molecular display, using ActiveICM.
Rotate the view using the left-click and drag. Translate by left-click+ctrl and drag
Zoom in by left-click and drag on the left-hand side of the screen. Crop left-click and drag on on the right-hand side of the screen.
Recentre using the button at the bottom of the plugin
As your first task: undisplay the protein and show a white background using the buttons below the ICM display.
The checkboxes to the left are used to show points of interest
Red: H-bond acceptors Blue: H-bond donors Cyan: Aromatic Brown: Hydrophobic
Stars Improving activity -> pharmacophore points that increase activity.
Cubes Reducing activity -> pharmacophore points that decrease activity.
Coloured by activity change BLUE to RED, LOW to HIGH
As your second task: check all three before progressing
The sliders to the left control the stars and cubes you have in the central display
Pharmacophore: The top slider selects the minimum and maximum number of pharmacophore changes between compounds
Activity: The bottom slider selects the minimum and maximum activity change between compounds
Update the change using the Refresh button
As your third task: show all activity increasing and decreasing points with an activity change between 0.4 and 1.0 and a number of pharmacophore between 1 and 4
The display and buttons to the right show the chemical changes and activity data for the points in the central display
Right-click and drag the mouse over the ICM display. A selected point will be highlighted in Green. Then click "Display compounds" to show the matched pairs
As your fourth task: show some matched pairs in the right-hand display
Error. You have not defined a compound to develop.
Type "1qmz" or a valid smiles string in the top search bar.
You can use OOMMPPAA to develop lead compounds
Type in a SMILES string and OOMMPPAA will search for compounds for this target. The most similar compound by Morgan fingerprint will be shown below.
Type in a PDB code and if this complex has been loaded the compound will be displayed in 3D below.
Two "Feature Maps" will appear on either side of the display.
Map one: shows the pharmacophoric conservation of the compound against compounds complexed for this target.
Map two: shows the fit of your compound to the Activity Increasing and Activity Reducing pharmacophore points
As your penultimate task: type "1qmz" into the search bar above and click Search or type enter
Error. You have not selected any points.
Right-click and drag to select a point or points.
Need a demo?Error. You have selected TOO MANY points.
Select fewer points or you will kill the server and be waiting FOREVER
Need a demo?Pharmacophoric conservation
Error. What you have entered is neither a valid pdb code nor a valid smiles string.