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Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI
- Source :
- Journal of Cheminformatics, Journal of Cheminformatics, Vol 4, Iss 1, p 22 (2012)
- Publication Year :
- 2012
- Publisher :
- Springer Science and Business Media LLC, 2012.
-
Abstract
- Background There are two line notations of chemical structures that have established themselves in the field: the SMILES string and the InChI string. The InChI aims to provide a unique, or canonical, identifier for chemical structures, while SMILES strings are widely used for storage and interchange of chemical structures, but no standard exists to generate a canonical SMILES string. Results I describe how to use the InChI canonicalisation to derive a canonical SMILES string in a straightforward way, either incorporating the InChI normalisations (Inchified SMILES) or not (Universal SMILES). This is the first description of a method to generate canonical SMILES that takes stereochemistry into account. When tested on the 1.1 m compounds in the ChEMBL database, and a 1 m compound subset of the PubChem Substance database, no canonicalisation failures were found with Inchified SMILES. Using Universal SMILES, 99.79% of the ChEMBL database was canonicalised successfully and 99.77% of the PubChem subset. Conclusions The InChI canonicalisation algorithm can successfully be used as the basis for a common standard for canonical SMILES. While challenges remain – such as the development of a standard aromatic model for SMILES – the ability to create the same SMILES using different toolkits will mean that for the first time it will be possible to easily compare the chemical models used by different toolkits.
- Subjects :
- Theoretical computer science
Chemical models
Computer science
Library and Information Sciences
computer.software_genre
Notation
lcsh:Chemistry
Physical and Theoretical Chemistry
Representation (mathematics)
lcsh:T58.5-58.64
Basis (linear algebra)
lcsh:Information technology
String (computer science)
SMILES
chEMBL
Computer Graphics and Computer-Aided Design
Computer Science Applications
Identifier
Canonicalisation
Line notations
lcsh:QD1-999
InChI
Data mining
computer
PubChem
Research Article
Subjects
Details
- ISSN :
- 17582946
- Volume :
- 4
- Database :
- OpenAIRE
- Journal :
- Journal of Cheminformatics
- Accession number :
- edsair.doi.dedup.....6eee65648ee747ae667e4fa229e6c32a