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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.




Singha S, Lahiri T, Dasgupta AK, Chakrabarti P., Structural Classification of Protein Using Surface Roughness Index, Onl J Bioinform., 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.