Hierarchical editing language for macromolecules
The Hierarchical Editing Language for Macromolecules (HELM) is a method of describing complex biological molecules. It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers.[1]
HELM was developed by a consortium of pharmaceutical companies in what is known as the Pistoia Alliance. Development began in 2008. In 2012 the notation was published openly and for free.[2]
The HELM open source project can be found on Github.[2]
The need for HELM became obvious as researchers began working on modeling and computational projects involving molecules and engineered biomolecules of this type. There was not a language to describe the entities in an accurate manner which described both the composition and the complex branching and structure common in these entity types.[1]
See also
- Simplified molecular-input line-entry system (SMILES)
- International Chemical Identifier (InChI)
- Molecular Query Language
- Molecule editor
- Chemical table file
- Molecular graphics
References
- ^ a b Zhang, Tianhong; Li, Hongli; Xi, Hualin; Stanton, Robert V.; Rotstein, Sergio H. (2012). "HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation". J. Chem. Inf. Model. 52 (10): 2796–2806. doi:10.1021/ci300192.
- ^ a b "About". OpenHELM.org. Retrieved 14 Nov 2014.