BioExcel Webinar #44: Clustering free energy landscapes from molecular dynamics simulations
Channel: BioExcel CoE
Date: 2020-05-12

Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This has remained a difficult task, despite a multitude of existing clustering methods. We present and discuss a few well-known clustering methods as well as InfleCS, a novel method for extracting well-defined core states from free energy landscapes. InfleCS identifies core states by exploiting a Gaussian mixture density estimator and the shape of the estimated density landscape. Finally, we apply the clustering on a molecular simulation of the Ca2+/CaM conformational ensemble and go through each step using a jupyter notebook tutorial.