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Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity

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Algorithms in Bioinformatics (WABI 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3692))

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Abstract

We present recent developments in efficiently maintaining the boundary and surface area of protein molecules as they undergo conformational changes. As the method that we devised keeps a highly accurate representation of the outer boundary surface and of the voids in the molecule, it can be useful in various applications, in particular in Monte Carlo Simulation. The current work continues and extends our previous work [10] and implements an efficient method for recalculating the surface area under conformational (and hence topological) changes based on techniques for efficient dynamic maintenance of graph connectivity. This method greatly improves the running time of our algorithm on most inputs, as we demonstrate in the experiments reported here.

Work reported in this paper has been supported in part by the IST Programme of the EU as Shared-cost RTD (FET Open) Project under Contract No IST-2001-39250 (MOVIE – Motion Planning in Virtual Environments), by The Israel Science Foundation founded by the Israel Academy of Sciences and Humanities (Center for Geometric Computing and its Applications), and by the Hermann Minkowski – Minerva Center for Geometry at Tel Aviv University.

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Author information

Authors and Affiliations

  1. School of Computer Science, Tel Aviv University, Israel

    Eran Eyal & Dan Halperin

Authors
  1. Eran Eyal
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  2. Dan Halperin
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Editor information

Editors and Affiliations

  1. Biocomputing Group, University of Bologna, Italy

    Rita Casadio

  2. Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA

    Gene Myers

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Eyal, E., Halperin, D. (2005). Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity. In: Casadio, R., Myers, G. (eds) Algorithms in Bioinformatics. WABI 2005. Lecture Notes in Computer Science(), vol 3692. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557067_33

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  • DOI: https://doi.org/10.1007/11557067_33

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29008-7

  • Online ISBN: 978-3-540-31812-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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