KM Prakash Lingam1, S Chandrakala2
1Anna University of Technology, Chennai, India.
2Dept. of Computer Science, Velammal Engineering College, Chennai, India.


Comparison of protein structures is an important tool for understanding the evolutionary relationships between proteins, predicting protein structures and thereby possibly predicting protein functions. This is referred to as structural alignment of proteins. Several methods of structural classification have been developed to introduce some order to the large amount of data present in the Protein Data Bank. Such methods facilitate structural comparisons and provide a greater understanding of structure and function. The most widely used and comprehensive databases are SCOP (Structural Classification of Proteins), CATH (Class Architecture Topology and Homology) and FSSP (Families of Structurally Similar Proteins) which represent three unique methods of classifying protein structures: purely manual, a combination of manual and automated, and purely automated, respectively. Most of the methods for protein structure alignment increase the quality of the alignment on the basis of geometric properties of the set of points representing the structures. Some of these methods compare the respective distance matrices of each structure to match the corresponding intramolecular distances for selected aligned substructures. The most direct approach to the comparison of two protein structures is to move the set of points representing one structure as a rigid body over the other, and look for equivalent residues. This can only be achieved for relatively similar structures and fails to detect local similarities of structures sharing common substructures. The commonly used metric for this purpose is the root-mean-square-deviation (RMSD) of aligned parts between two structures has been commonly used to measure the similarity between pairs of protein structures after they are superimposed. This paper attemps to give an overview of recent approaches in protein structure comparison methods and the challenges commonly deployed to assess the structure alignment of proteins. Read More …

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