Web Services Manual
Find scaffold for a data set
The common substructure function, now available both as a Daylight Web Service and as part of the Daylight Toolkit Package, allows one to take a set of structures represented as SMILESTM and generates a SMARTS® scaffold that captures all common substructure elements of that set.
In contrast to a traditional maximum common substructure (MCS), the SMARTS® scaffold may contain multiple fragments of common substructure. The user can control the level of topology used (with or without ring bond counts) and a minimum fragment size to eliminate fragments of the scaffolds that are smaller than the minimum.