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International Conference: Beyond Databases, Architectures and Structures

BDAS 2019: Beyond Databases, Architectures and Structures. Paving the Road to Smart Data Processing and Analysis pp 233–247Cite as

A Novel Approach for Fast Protein Structure Comparison and Heuristic Structure Database Searching Based on Residue EigenRank Scores

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Part of the book series: Communications in Computer and Information Science ((CCIS,volume 1018))

Abstract

With the rapid growth of public protein structure databases, computational techniques for storing as well as comparing proteins in an efficient manner are still in demand. Proteins play a major role in virtually all processes in life, and comparing their three-dimensional structures is essential to understanding the functional and evolutionary relationships between them.

In this study, a novel approach to compute three-dimensional protein structure alignments by means of so-called EigenRank score profiles is proposed. These scores are obtained by utilizing the LeaderRank algorithm—a vertex centrality indexing scheme originally introduced to infer the opinion leading role of individual actors in social networks. The obtained EigenRank representation of a given structure is not just highly-specific, but can also be used to compute profile alignments from which three-dimensional structure alignments can be rapidly deduced. This technique thus could provide a tool to rapidly scan entire databases containing thousands of structures.

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Notes

  1. 1.

    The set of adjacency matrices can actually be used to derive one single matrix containing binned residue-residue distances. The underlying structure of the protein can be reconstructed from that matrix.

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Author information

Authors and Affiliations

  1. Bioinformatics Group, University of Applied Sciences Mittweida, Technikumplatz 17, 09648, Mittweida, Germany

    Florian Heinke, Lars Hempel & Dirk Labudde

  2. TU Bergakademie Freiberg, Akademiestrasse 6, 09599, Freiberg, Germany

    Florian Heinke

  3. Fraunhofer Cybersecurity, Darmstadt, Germany

    Dirk Labudde

Authors
  1. Florian Heinke
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  2. Lars Hempel
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  3. Dirk Labudde
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Corresponding author

Correspondence to Florian Heinke .

Editor information

Editors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Stanisław Kozielski

  2. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Dariusz Mrozek

  3. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Paweł Kasprowski

  4. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Bożena Małysiak-Mrozek

  5. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Daniel Kostrzewa

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Heinke, F., Hempel, L., Labudde, D. (2019). A Novel Approach for Fast Protein Structure Comparison and Heuristic Structure Database Searching Based on Residue EigenRank Scores. In: Kozielski, S., Mrozek, D., Kasprowski, P., Małysiak-Mrozek, B., Kostrzewa, D. (eds) Beyond Databases, Architectures and Structures. Paving the Road to Smart Data Processing and Analysis. BDAS 2019. Communications in Computer and Information Science, vol 1018. Springer, Cham. https://doi.org/10.1007/978-3-030-19093-4_18

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  • DOI: https://doi.org/10.1007/978-3-030-19093-4_18

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-19092-7

  • Online ISBN: 978-3-030-19093-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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