Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison

Frédéric Cazals 1 Tom Dreyfus 1 Dorian Mazauric 1, 2 Andrea Roth 1 Charles Robert 3
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
2 GEOMETRICA - Geometric computing
CRISAM - Inria Sophia Antipolis - Méditerranée , Inria Saclay - Ile de France
Abstract : We present novel algorithms and software addressing four core problemsin computational structural biology, namely analyzing a conformationalensemble, comparing two conformational ensembles, analyzing a sampledenergy landscape, and comparing two sampled energy landscapes. Usingrecent developments in computational topology, graph theory, andcombinatorial optimization, we make two notable contributions. First,we a present a generic algorithm analyzing height fields. We then usethis algorithm to perform density based clustering of conformations,and to analyze a sampled energy landscape in terms of basins andtransitions between them. In both cases, topological persistence isused to manage ruggedness. Second, we introduce two algorithms tocompare transition graphs. The first is the classical earth mover distance metric which depends only on local minimum energyconfigurations along with their statistical weights, while the secondincorporates topological constraints inherent to conformationaltransitions.Illustrations are provided on a simplified protein model (BLN69), whosefrustrated potential energy landscape has been thoroughly studied.The software implementing our tools is also made available, and shouldprove valuable wherever conformational ensembles and energy landscapesare used.
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[Research Report] RR-8610, INRIA. 2014
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Contributeur : Frederic Cazals <>
Soumis le : jeudi 27 octobre 2016 - 15:58:25
Dernière modification le : jeudi 9 février 2017 - 15:47:37

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Frédéric Cazals, Tom Dreyfus, Dorian Mazauric, Andrea Roth, Charles Robert. Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison. [Research Report] RR-8610, INRIA. 2014. <hal-01076317v3>

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