Conformational ensembles and sampled energy landscapes: Analysis and comparison
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Updated: Apr 12, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
Published on: April 8, 2020
Frédéric Cazals1, Tom Dreyfus1, Dorian Mazauric1
1Inria 2004 route des Lucioles, BP 93, F-06902 Sophia-Antipolis, FRANCE.
Abstract:
We present novel algorithms and software addressing four core problems in computational structural biology, namely analyzing a conformational ensemble, comparing two conformational ensembles, analyzing a sampled energy landscape, and comparing two sampled energy landscapes. Using recent developments in computational topology, graph theory, and combinatorial optimization, we make two notable contributions. First, we present a generic algorithm analyzing height fields. We then use this algorithm to perform density-based clustering of conformations, and to analyze a sampled energy landscape in terms of basins and transitions between them. In both cases, topological persistence is used to manage (geometric) frustration. Second, we introduce two algorithms to compare transition graphs. The first is the classical earth mover distance metric which depends only on local minimum energy configurations along with their statistical weights, while the second incorporates topological constraints inherent to conformational transitions. Illustrations are provided on a simplified protein model (BLN69), whose frustrated potential energy landscape has been thoroughly studied. The software implementing our tools is also made available, and should prove valuable wherever conformational ensembles and energy landscapes are used.
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