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Web Services Manual
Clustering Manual
R-table Generation
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.