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

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.

• Publication year

  2011

• Venue

  Journal of Cheminformatics

• Publication date

  2011-01-07

• Fields of study

  Medicine, Chemistry, Computer Science

• Identifiers
  DOI 10.1186/1758-2946-3-1PMID 21214931PMCID 3027187
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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