On Using Energy Signatures in Protein Structure Similarity Searching

Authors:
Bożena Małysiak;Alina Momot;Stanisław Kozielski;Dariusz Mrozek
Affiliations:
Department of Computer Science, Silesian University of Technology, Gliwice, Poland 44-100;Department of Computer Science, Silesian University of Technology, Gliwice, Poland 44-100;Department of Computer Science, Silesian University of Technology, Gliwice, Poland 44-100;Department of Computer Science, Silesian University of Technology, Gliwice, Poland 44-100
Venue:
ICAISC '08 Proceedings of the 9th international conference on Artificial Intelligence and Soft Computing
Year:
2006

Citing 2
Cited 1

CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features

CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
EAST: energy alignment search tool

FSKD'06 Proceedings of the Third international conference on Fuzzy Systems and Knowledge Discovery

Protein Comparison by the Alignment of Fuzzy Energy Signatures

RSKT '09 Proceedings of the 4th International Conference on Rough Sets and Knowledge Technology

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Abstract

The analysis of small molecular substructures (like enzyme active sites) in the whole protein structure can be supported by using methods of similarity searching. These methods allow to search the 3D structural patterns in a database of protein structures. However, the well-known methods of fold similarity searching like VAST or DALI are not appropriate for this task. Methods that benefit from a dependency between a spatial conformation and potential energy of protein structure seem to be more supportive. In the paper, we present a new version of the EAST (Energy Alignment Search Tool) algorithm that uses energy signatures in the process of similarity searching. This makes the algorithm not only more sensitive, but also eliminates disadvantages of previous implementations of our EAST method.