Physicochemical Property Labels as Molecular Descriptors for Improved Analysis of Compound–Protein and Compound–Compound Networks

Abstract

Small molecules can be represented in various file formats, (1) one-line systems such as SMILES (Simplified Molecular Input Line Entry System) and InChI (International Chemical Identifier) and (2) table systems such as the molfiles, SDF (Structure Data File), and KCF (KEGG Chemical Function). KCF and KCF-S (KEGG Chemical Function-and-Substructures) apply physicochemical property labels on the representations of small molecules, and contribute to improved analysis of compound–protein networks including drug–target interaction, and compound–compound networks including metabolic pathways. In this chapter, the main concepts, usage, and some example applications of the KCFCO and KCF-S packages are explained.