The process for building a query is much the same as that of Build and Run:
The difference is that the workflow stops after editing the fragment and allows you to save the query.
The first step in creating a BROOD query is to load or create a source molecule. The molecule can be loaded from a file, entered by name, or sketched in the sketcher.
A protein can be loaded to provide a bump-check for generated results, although protein chemistry is not used as part of the score. You can also specify a selection protein, which requires a protein atom to be close to the query as a simplistic screen for selectivity.
Below the protein text entry boxes, vBROOD displays the properties of the loaded molecule. Any properties that vBROOD determines might need attention are highlighted in red.
After loading or creating a molecule, vBROOD will display the 2D structure. You must then select some portion of the molecule for replacement. You can select the fragment to be replaced in two ways:
|Fragment-based selection||Lasso selection|
Some molecules may need additional fixes for problems found when they are loaded or selected. vBROOD highlights any problematic atom or bond and displays a message in the lower-right corner. If the message is red, the problem must be fixed before you can continue to build the query. Messages in yellow can be ignored, but usually should be addressed as they may lead to unexpected behaviors.
The following are examples of some problems and their fixes
BROOD requires the specification of certain types of stereochemistry. Ignoring this problem can result in issues with coordinate generation or with property filtering. To fix unspecified stereochemistries, right-click on the red highlighted atom or bond and select Set Chirality or Set Bond Stereo and choose the appropriate stereochemistry.
BROOD does not allow double bonds to be broken by selection. To correct this problem, either click Select Bond or redo the selection.
Broken aliphatic rings can be ignored (but will always be closed), but broken aromatic rings must be fixed. To do this, either click Select Ring button or redo the selection.
BROOD’s default databases have between one and three attachment points. Unless you are using a custom fragment database, BROOD will not produce any results when you use a query with four or more attachments. Redo the selection so that it has between one and three attachment points or generate and use a non-default database that includes fragments with four attachment points.
Selecting two atoms that are each bonded to a third, unselected atom results in two attachment points overlapping. To correct this, click Fix or redo the selection.
vBROOD requires you to select some fraction of the molecule or it will not continue. To fix this, select a fragment of the molecule.
Once a molecule has a valid selection and all problems have been resolved, the Next button will be enabled. Click Next to advance to the Edit Fragment step.
The Edit Fragment step allows users to edit some aspects of the replacement query. You can add and remove color atoms, add and remove constraints, or remove atoms in the query. This step also displays the query structure in 3D as well as the attachment vectors as R-group atoms. Color atoms are displayed as large spheres patterned and colored according to the color atom type. Constraint atoms are displayed as colored and patterned rings with a diameter corresponding to the diameter of the constraint.
The Fragment Editor provides five tools for editing a query, shown as icons on the left side of the 3D window:
If the query includes a protein, it is also possible to toggle the visibility of the protein with the Show Protein and Hide Protein buttons.
Color atoms allow users to specify desired chemistry at specific places on the fragment. Adding a color atom to a molecule is simple:
Either color atoms or molecular atoms can be selected. Multiple color atoms placed in the same location are displayed as slices of the same color atom sphere. By placing the same type of color atom at the same location, color atoms may be weighted to increase their influence on the score.
To place a color atom in between one or more atoms, hold the Shift key while clicking additional atoms. The color atom will be placed at the center of mass of the selected group.
|The constraint menu||A constraint|
A constraint is much like a color atom in that it represents desired chemical features. Unlike a color atom, however, a constraint is a requirement, not a component of the score. Adding a constraint to a molecule is largely the same as adding a color atom:
As with color atoms, to place a constraint in between one or more atoms, hold the Shift key while clicking additional atoms. The constraint will be placed at the center of mass of the selected group.
|The custom constraint dialog||The custom SMARTS dialog|
Custom constraints can also be defined with user-supplied SMARTS patterns. To define a new constraint type, select Add Custom Constraint. The Add Custom Constraint dialog prompts for a constraint name, a constraint SMARTS pattern, and a radius. SMARTS patterns can be either typed in the SMARTS text edit or selected from the SMARTS dialog by clicking the + button in the SMARTS text edit.
Once these steps have been completed, click Next to progress to the next page.