Structure-based querying of proteins using wavelets

The ability to retrieve molecules based on structural similarity has use in many applications, from disease diagnosis and treatment to drug discovery and design. In this paper, we present a method to represent protein molecules that allows for the fast, flexible and efficient retrieval of similar structures, based on either global or local attributes. We begin by computing the pair-wise distance between amino acids, transforming each 3D structure into a 2D distance matrix. We normalize this matrix to a specific size and apply a 2D wavelet decomposition to generate a set of approximation coefficients, which serves as our global feature vector. This transformation reduces the overall dimensionality of the data while still preserving spatial features and correlations. We test our method by running queries on three different protein datasets that have been used previously in the literature, basing our comparisons on labels taken from the SCOP database. We find that our method significantl...

• Type: Conference
• Year: 2006
• Where: CIKM
• Authors: Keith Marsolo, Srinivasan Parthasarathy, Kotagiri Ramamohanarao
• Keywords: 2D Wavelet Decomposition, CIKM 2006, Information Management, Proteins, We Begin