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Maxent-Stress Optimization of 3D Biomolecular Models

Authors Michael Wegner, Oskar Taubert, Alexander Schug, Henning Meyerhenke

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Michael Wegner
Oskar Taubert
Alexander Schug
Henning Meyerhenke

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Michael Wegner, Oskar Taubert, Alexander Schug, and Henning Meyerhenke. Maxent-Stress Optimization of 3D Biomolecular Models. In 25th Annual European Symposium on Algorithms (ESA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 87, pp. 70:1-70:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
https://doi.org/10.4230/LIPIcs.ESA.2017.70

Abstract

Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not directly provide 3D structures; instead they typically yield noisy and erroneous distance information between specific entities such as atoms or residues, which have to be translated into consistent 3D models. Here we present an approach for this translation process based on maxent-stress optimization. Our new approach extends the original graph drawing method for the new application's specifics by introducing additional constraints and confidence values as well as algorithmic components. Extensive experiments demonstrate that our approach infers structural models (i.e., sensible 3D coordinates for the molecule's atoms) that correspond well to the distance information, can handle noisy and error-prone data, and is considerably faster than established tools. Our results promise to allow domain scientists nearly-interactive structural modeling based on distance constraints.
Keywords
  • Distance geometry
  • protein structure determination
  • 3D graph drawing
  • maxent-stress optimization

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