Web Services Manual
R-groups determined for scaffold-based cluster
One of the most common methods to study and to report structure-activity relationships within a set of structures is to represent the set as an R-table with a common scaffold and variable R-groups for each structure.
The new generateRTable program, available as a Daylight Web Service, generates an optimal R-table from a set of structures and a scaffold. There are three ways to construct the input: 1) use the deriveSDClusters web service to generate the required cluster information directly, 2) use your own structure sets (clusters) and the deriveScaffold web service, or 3) input your own structure set and your own scaffold.
The scaffold is a SMARTS® expression that contains the structural features common to all members of the cluster. With the potential for multiple fragments, it is possible to examine variable linking groups.
R-group determination is optimized so that, wherever possible, the scaffold is oriented to allow R-groups with similar properties to be placed in the same column of the R-table. R-groups may have multiple attachment points to the scaffold making it possible to examine ring substitutions (X-groups).
This new web service extends the utility of the deriveScaffold and the deriveSDCluster web services by representing sets of structures in the most useful manner. It complements the getDepiction web service, which can highlight a set of structures with a common scaffold. Together, these web services provide essential analysis tools for lead identification and lead optimization.