Energy profiles in detection of protein structure modifications

Mrozek, Dariusz; Małysiak, Bożena; Kozielski, Stanisław

doi:10.1109/icoci.2006.5276462

Cited by 6 publications

(1 citation statement)

References 16 publications

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“…In our research on protein activities in cellular reactions [9], [10], [11], we usually look for regions that are biologically important modules, e.g active sites of enzymes, or search for regions of conformation switching.…”

Section: Introductionmentioning

confidence: 99%

Alignment of protein structure energy patterns represented as sequences of Fuzzy Numbers

Mrozek

Kozielski

2009

NAFIPS 2009 - 2009 Annual Meeting of the North American Fuzzy Information Processing Society

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The comparative analysis of structural and energy features of proteins can be a key to understand how proteins work and interact to each other in cellular reactions. Potential energy, which is a function of atomic positions in a protein structure, can be used to describe molecule's abilities to interact with other biological molecules. Potential energy characteristics are supportive in searching similar, biologically important molecular regions that have similar functions in different organisms or organs. In the paper, we present the similarity searching method, which base on the alignment of energy patterns. In the alignment phase energy patterns are represented as sequences of fuzzy numbers. This increases the fault-tolerance of the alignment and ensures the approximate character of the method. The alignment of fuzzy sequences is one of the main steps in the new FN-EAST method (Fuzzy Numbers -Energy Alignment Search Tool). The FN-EAST allows to seek similar structural regions represented as energy patterns. The new alignment incorporated in the similarity searching eliminates some weaknesses of the FN-EAST predecessors.

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Section: Introductionmentioning

confidence: 99%