Advanced clustering methods for identifying bioactive molecular conformations

Angiotensin II is a hormone, which plays a vital role in the regulation of blood pressure, in the conservation of total blood volume, and salt homeostasis. Previous studies of AII bioactive conformation, when bound to the AT1 receptor, appeared to have diverging results making it important to study the intermolecular interactions of AII. In this work we investigate the bioactive conformation of AII, using multiple trajectories from simulations, with Markov State Models (MSM). Also, we validate the efficiency of an inverted-quantized k-means algorithm (IQ-means), as a fast approximate clustering technique, on data from trajectories of MD simulations with reasonable trade-offs between time and accuracy. Finally, we experiment on Markov State Models using various clustering techniques for the generation of microstates (IQ-means), macrostates and for the selection of the macrostate representatives (GROMOS).