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OJB®
Online Journal of Bioinformatics ©
Volume 7 (2):74-84, 2006
Structural Classification of Protein Using Surface
Roughness Index
Singha S1, Lahiri
T1*, Dasgupta AK2, Chakrabarti P3.
1Bioinformatics
Division,
Indian Institute of Information Technology, Allahabad
and 2Department of Biochemistry, Calcutta
University and 3Department of Biochemistry, Bose
Institute, P1/12 CIT Scheme VIIM, Kolkata- 700 054,
India.
ABSTRACT
Singha S, Lahiri
T, Dasgupta AK, Chakrabarti
P., Structural Classification of Protein Using Surface Roughness Index, Online
J Bioinformatics, 7 (2):74-84, 2006. A protein structural classification using surface
roughness properties is described. A protein surface characterizing parameter, Surface Roughness Index was designed
which is made as an invariant measure of surface geometry with respect to any
orientation of a protein. It was found that the topology of protein can
be described from the angle of its surface-roughness property which can serve
to identify a protein. Structural Classification of Proteins (SCOP)
classify protein into classes-folds-superfamilies-families
which correlated with the proposed classifier system to a reasonable extend.
The deviation from the classification result yielded by the proposed method
from that of the SCOP is explained and the significance of the information
mined from this deviation from SCOP is discussed.
KEYWORDS Classifier system, Invariant measure, SCOP, Surface
Roughness Index.