While the Bemis–Murcko approach has dominated scaffold analysis for the past few decades, it has its shortcomings - for example, chemical reaction information is not considered.
With this in mind, Dilyana Dimova et al. (Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany) sought to determine a consistent and generally applicable scaffold definition able to take compound series and chemical reaction information into account.
Their work is published open access in Future Science OA, and through it you can access their database of 12000 analog series-based scaffolds are made freely available for medicinal chemistry and chemical informatics applications.
Citation: Dilyana Dimova, Dagmar Stumpfe, Ye Hu, Jürgen Bajorath. Analog series-based scaffolds: computational design and exploration of a new type of molecular scaffolds for medicinal chemistry. Future Sci. OA FSO149 doi:10.4155/fsoa-2016-0058 (2016).