We encourage interested readers to consult two recent publications by the Rarey lab:
- Diedrich, K., Graef, J., Schöning-Stierand, K., & Rarey, M. (2020). GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank. Bioinformatics. (https://doi.org/10.1093/b...)
- Inhester, T., Bietz, S., Hilbig, M., Schmidt, R., & Rarey, M. (2017). Index-based searching of interaction patterns in large collections of protein–ligand interfaces. Journal of chemical information and modeling, 57(2), 148-158. (https://doi.org/10.1021/a...)
We strongly believe that readers will benefit from this method and literature, especially given the low number of relevant publications on structural motif/pattern searching in recent years.
GeoMine is freely available as part of the ProteinsPlus portal: https://proteins.plus.