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

  • Masaaki KoteraEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1825)

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 compoundprotein networks including drugtarget interaction, and compoundcompound networks including metabolic pathways. In this chapter, the main concepts, usage, and some example applications of the KCFCO and KCF-S packages are explained.

Key words

Molecular file formats Chemical fingerprints Chemical descriptors Compound–protein network Drug–target interaction Compound–compound network Metabolic pathway 

Notes

Acknowledgments

Funding from the Ministry of Education, Culture, Sports, Science and Technology of Japan, the Japan Science and Technology Agency, and the Japan Society for the Promotion of Science; JSPS Kakenhi (25108714,). This work was also supported by the Program to Disseminate Tenure Tracking System, MEXT, Japan.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Chemical System Engineering, School of EngineeringThe University of TokyoTokyoJapan

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