There is currently no specific technical publication to reference regarding the new generation of the CSD web interface, including either simple searching or substructure searching. If you are making use of CSD data in a publication, please cite the CSD reference paper:
The Cambridge Structural Database C. R. Groom, I. J. Bruno, M. P. Lightfoot, S. C. Ward, Acta Cryst. (2016) B72, 171-179. DOI: 10.1107/S2052520616003954
If you so choose, the following may be used to cite the CSD web interface itself:
CCDC (2017). CSD web interface – intuitive, cross-platform, web-based access to CSD data. Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, UK.