DBsimilarity

DBsimilarity is a method proposed in a scientific paper to help natural product researchers analyze chemical data obtained from databases. This method involves organizing structural databases into similarity networks to represent the chemical space of a given organism or biological system. The method includes various steps such as converting .sdf files into .csv files, adding chemoinformatics data, constructing a custom database for rapid dereplication of MS data on MZMine, constructing a candidate list of compounds for rapid dereplication of 2D NMR data on NMRfilter, calculating similarities between compounds, and convert this square matrix into a network type of file. Cytoscape is suggested as an ideal platform for visualizing similarity networks, and Jupyter Notebooks are recommended for their readability to assist users in developing valuable programming skills. The ultimate goal of this method is to help researchers better understand the rich information available from a list of compounds found in a specimen.