Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric

Abstract

Discerning the similarity between two molecules is a challenging problem in drug discovery as well as in molecular biology.

Chemical Molecules Search Based on Graph Similarity Measure

“…Elinor Velasquez et al [7] presented a Wavelet-based Riemannian metric for determining molecular similarity. The proposed metric extends traditional molecular similarity measures in terms of its ability to capture and compare nonlinear molecular descriptors, thus allowing more accurate characterization of the true nature of the factors involved.…”

Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels

“…An often employed principle in chemistry is that compounds with similar structures have similar biochemical properties [29,2,12,8,27]. This principle has been successfully applied in different areas, such as drug discovery [24,9] and enzyme-promiscuity prediction [20], in which data from experimentally measured compounds is used to make predictions about the properties of a compound currently being investigated.…”

Metrics for measuring distances in configuration spaces

“…Diversity analysis is at the heart of any structure prediction method in material science and solid state physics [1][2][3][4][5] and conformer search in structural biology and drug discovery. [6][7][8][9][10][11][12] In the latter case, most of the proposed approaches [13][14][15] use approximate methods that reduce the structure description information, e.g. by excluding the side chains in a protein or a two dimensional representations of the molecule, [16] to speed up the searching procedure.…”