TY - GEN
T1 - Alignment of protein structure energy patterns represented as sequences of fuzzy numbers
AU - Mrozek, Dariusz
AU - Małysiak-Mrozek, Bozena
AU - Kozielski, Stanisław
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
KW - Force fields
KW - Molecular mechanics
KW - Protein structures
KW - Similarity searching
UR - https://www.scopus.com/pages/publications/70350414422
U2 - 10.1109/NAFIPS.2009.5156391
DO - 10.1109/NAFIPS.2009.5156391
M3 - Conference contribution
AN - SCOPUS:70350414422
SN - 9781424445776
T3 - Annual Conference of the North American Fuzzy Information Processing Society - NAFIPS
BT - NAFIPS 2009 - 2009 Annual Meeting of the North American Fuzzy Information Processing Society
T2 - 2009 Annual Meeting of the North American Fuzzy Information Processing Society, NAFIPS 2009
Y2 - 14 June 2009 through 17 June 2009
ER -