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]
HELM
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] Protein sequences can describe larger proteins and chemical language files such as mol files can describe simple peptides. However, the complexity of new research biomolecules makes describing large complex molecules difficult with chemical formats, and peptide formats arent flexible to describe non-natural amino acids and other chemistries.[3]
In HELM, molecules are represented at a monomer level (instead of an atom level). Monomers are assigned short unique identifiers in a central HELM database and can be represented by the identifier in strings. The approach is similar to that used in Simplified molecular-input line-entry system (SMILES).[4]
In 2014 ChEMBL announced plans to adopt HELM by 2014.[5]
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 composed of informatics experts and researchers from industry, academia and life science service organizations. [6]
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.
- ^ "HELM in ChEMBL". Feb 2014. Retrieved 17 Nov 2014.
- ^ Krol, Aaron (18 Jul 2014). "Universal Language: The Pistoia Alliance Takes on Indescribable Biology". http://www.bio-itworld.com/. Retrieved 17 Nov 2014.
{{cite web}}: External link in|website= - ^ "The Pistoia Alliance and EMBL-EBI announce HELM collaboration for cheminformatics". http://www.ebi.ac.uk/. Retrieved 17 Nov 2014.
{{cite web}}: External link in|website= - ^ "Mission&History". http://www.pistoiaalliance.org/. Retrieved 15 Nov 2014.
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