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]
Pistoia Alliance
At a conference in Pistoia, Italy, a group of researchers from Pfizer AstraZeneca, GlaxoSmithKline, and Novartis formed what came to be known as the Pistoia Alliance. All parties were interested in solving problems for data aggregation, data sharing and analytics for pharmaceutical research. The alliance was incorporated in 2008. The alliance is now comprised of informatics experts and researchers from industry, academia and life science service organizations. [3]
See also
- Simplified molecular-input line-entry system (SMILES)
- International Chemical Identifier (InChI)
- Molecular Query Language
- Molecule editor
- Chemical table file
- Molecular graphics
- FASTA
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.
- ^ "Mission&History". http://www.pistoiaalliance.org/. Retrieved 15 Nov 2014.
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