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

: Heinke, F.; Hempel, L.; Labudde, D.


Kozielski, S.:
Beyond databases, architectures and structures : Paving the road to smart data processing and analysis : 15th International Conference, BDAS 2019, Ustroń, Poland, May 28-31, 2019 : proceedings
Cham: Springer International Publishing, 2019 (Communications in computer and information science 1018)
ISBN: 978-3-030-19093-4
ISBN: 978-3-030-19092-7
International Conference "Beyond Databases, Architectures and Structures" (BDAS) <15, 2019, Ustron>
Fraunhofer SIT ()

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.