BPCPPDYSOE21 – scientific programme
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BP: Fachverband Biologische Physik
BP 24: Poster B: Active Biological Matter, Cell Mechanics, Systems Biology, Computational Biophysics, etc.
BP 24.49: Poster
Tuesday, March 23, 2021, 16:00–18:30, BPp
Exploratory analysis and comparison of biomolecular structural ensembles with PENSA — •Martin Vögele1 and Ron O. Dror1,2,3,4 — 1Department of Computer Science, Stanford University — 2Department of Molecular and Cellular Physiology, Stanford University — 3Department of Structural Biology, Stanford University — 4Institute for Computational and Mathematical Engineering, Stanford University
Molecular simulations enable the study of proteins and other biomolecules and their dynamics on an atomistic scale. The large amount of data produced for ever more complex systems often makes it difficult to identify the structural features that are relevant for a particular phenomenon. Whilst most available analysis tools provide methods to analyze one simulation at a time, many common research pursuits necessitate analysis across several conditions - like mutations or different ligands - and finding significant differences between them.
We introduce PENSA, a collection of methods for exploratory analysis and comparison of structural ensembles such as those from molecular dynamics simulations. So far PENSA users can compare two conditions, e.g., via the relative entropy of their features or a Kolmogorov-Smirnov test, and visualize deviations on a reference structure. PENSA also implements exploratory analysis methods - like principal component analysis and clustering - that are applied across several ensembles. We demonstrate PENSA's usefulness on real-world examples by showing how it helps to determine molecular mechanisms efficiently.