BioExcel Webinar #44 - Clustering free energy landscapes from molecular dynamics simulations
| Main Authors: | Delemotte, Lucie, Westerlund, Annie |
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| Format: | info Proceeding eJournal |
| Terbitan: |
, 2020
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/3824057 |
Daftar Isi:
- 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.