A hybrid approach for indexing and searching protein structures

Abstract

Searching for structural similarities of proteins has a central role in bioinformatics. Most tasks of bioinformatics depends on investigating the homologous protein's sequence or structure these tasks vary from predicting the protein structure to determine sites in protein structure where drug can be attached. Protein structure comparison problem is extremely important in many tasks. It can be used for determining function of protein, for clustering a given set of proteins by their structure, for assessment in protein fold prediction. Protein Structure Indexing using Suffix Array and Wavelet (PSISAW) is a hybrid approach that provides the ability to retrieve similarities of proteins based on their structures. Indexing the protein structure is one approach of searching for protein similarities. The suffix arrays are used to index protein structure and the wavelet is used to compress the indexed database. Compressing the indexed database is supposed to make the searching time faster and memory usage lower but it affects the accuracy with accepted rate of error.The experimental results, which are based on the structural classification of proteins (SCOP) dataset, show that the proposed approach outperforms existing similar techniques in memory utilization and searching speed. The results show an enhancement in the memory usage with factor 50%.