[hal-01076317] Conformational Ensembles and Sampled Energy Landscapes Analysis and Comparison

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 a 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 ruggedness 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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