CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

By Axel Drefahl. Journal of Cheminformatics, 2011

409 citations recorded by the source corpus.

CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. Annotations are enclosed in curly braces and anchored to an atomic node or at the end of the molecular graph depending on the annotation type. CurlySMILES includes predefined annotations for stereogenicity, electron delocalization charges, extra-molecular interactions and connectivity, surface attachment, solutions, and crystal structures and allows extensions for domain-specific annotations. CurlySMILES provides a shorthand format to encode molecules with repetitive substructural parts or motifs such as monomer units in macromolecules and amino acids in peptide chains. CurlySMILES further accommodates special formats for non-molecular materials that are commonly denoted by composition of atoms or substructures rather than complete atom connectivity.

Subfields: Biomedical Engineering, Catalysis, Materials Chemistry

View Paper: https://www.semanticscholar.org/paper/5a1e5e8dc9cb77eb9d0cabdd4854ff926bb80f72

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In Catalysis

Alán Aspuru-Guzik

In Materials Chemistry

Citations in the corpus

Optimizing distributions over molecular space. An Objective-Reinforced Generative Adversarial Network for Inverse-design Chemistry (ORGANIC) (2017, background): “There are possibly better textual representations for diﬀerent chemistry domains [43], future work will also look at overcoming SMILES validation problems with grammar aware networks[44].”