Assessing kinase similarity, or how to avoid side effects?
Kinases are highly conserved in their binding site, which presents a challenge since one ligand may bind not only the designated target (on-target) but also other targets (off-targets), causing mild to severe sides effects. Being able to assess kinase similarity could therefore give insight into potential side-effects.
The proposed pipeline, part of the TeachOpenCADD project, allows the study of kinase similarities from four different angles in an automated and modular fashion.
A short kinase introduction, as well as an overall conclusion, are part of the special kinase edition, establishing 6 new notebooks! The analysis of kinase similarity uses information from:
- pocket sequence (from KLIFS),
- pocket structure (using the KiSSim fingerprint),
- protein-ligand interactions (using the OpenCADD extension of KLIFS), and
- ligand-profiling data (from the ChEMBL database, queried with Kinodata).
Here’s the link to this collection: https://projects.volkamerlab.org/teachopencadd/talktorials.html#kinase-similarity.