BioExcel Webinar #44: Clustering free energy landscapes from molecular dynamics simulations

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.

Видео BioExcel Webinar #44: Clustering free energy landscapes from molecular dynamics simulations канала BioExcel CoE