yaInChI: Modified InChI string scheme for line notation of chemical structures

Abstract

A modified InChI (International Chemical Identifier) string scheme, yaInChI (yet another InChI), is suggested as a method for including the structural information of a given molecule, making it straightforward and more easily readable. The yaInChI theme is applicable for checking the structural identity with higher sensitivity and generating three-dimensional (3-D) structures from the one-dimensional (1-D) string with less ambiguity than the general InChI method. The modifications to yaInChI provide non-rotatable single bonds, stereochemistry of organometallic compounds, allene and cumulene, and parity of atoms with a lone pair. Additionally, yaInChI better preserves the original information of the given input file (SDF) using the protonation information, hydrogen count +1, and original bond type, which are not considered or restrictively considered in InChI and SMILES. When yaInChI is used to perform a duplication check on a 3D chemical structure database, Ligand.Info, it shows more discriminating power than InChI. The structural information provided by yaInChI is in a compact format, making it a promising solution for handling large chemical structure databases.

Keywords:

• line notation
• duplication check
• InChI
• chemical database
• SMILES

Acknowledgements

This work was supported by the Human Resources Development of the Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Ministry of Knowledge Economy, Republic of Korea (No. 20104010100610) and a grant of the Korea Healthcare Technology R & D Project, Ministry for Health, Welfare & Family Affairs, Republic of Korea (No. A100096).