2025-143-13

Large-Scale Analysis of Ligand-Target Interactions of Rho-associated protein kinase 1

Vedoucí práce: Ing. Martin Šícho, Ph.D.

Konzultant: M.Sc. Wim Dehaen, Ph.D.

Podstata a cíl práce

Rho-associated protein kinase 1 (ROCK1) is a protein serine/threonine kinase that plays a crucial role in various cellular functions, making it clinically relevant in several areas. ROCK1 has been implicated in cancer, cardiovascular diseases and inflammatory response. In this context, this thesis project will use the tools of structure-based drug design by performing docking of known ligands and decoys to the 3D model of ROCK1. Clustering of binding poses will be performed based on interaction fingerprints in order to determine differences in binding between active and inactive compounds. Based on this analysis, a structure-based virtual screening workflow will be suggested to find novel ligands of ROCK1 based on the analysis.

Náplň činnosti studenta

The student will study available literature and data on ROCK1 and assemble a data set of known binders and non-binders. They will also analyze publicly available 3D models of ROCK1 and select the best ones to use in the study. Lastly, the student will take advantage of an existing docking workflow and adapt it to the case of ROCK1 in order to determine binding modes and suggest the best virtual screening strategy.

Doplňující informace

Místo řešení: Ústav informatiky a chemie (143)

Téma je možné zvolit pro následující specializace