Hierarchical Editing Language for Macromolecules

Abbreviation: HELM

General Information

HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules (e.g. proteins, nucleotides, antibody drug conjugates) whose size and complexity render existing small-molecule and sequence-based informatics methodologies impractical or unusable. HELM solves this problem through a hierarchical notation that represents complex macromolecules as polymeric structures with support for unnatural components (e.g. unnatural amino acids) and chemical modifications.

Homepage http://www.OpenHELM.org

Developed in Denmark , France , Germany , Hungary , Switzerland , United Kingdom , United States

Created in 2013

Taxonomic range

Not applicable

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: HELM; Hierarchical Editing Language for Macromolecules; DOI: https://doi.org/10.25504/FAIRsharing.pDq8lX; Last edited: Jan. 8, 2019, 1:39 p.m.; Last accessed: Apr 21 2019 3:07 a.m.

This record is maintained by HELMInfo (MacroMol)

Record added: July 18, 2018, 4:44 p.m.
Record updated: July 19, 2018, 1:16 p.m. by The FAIRsharing Team.

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Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'The FAIRsharing Team' at 13:16, 19 Jul 2018 (approved):

	'domains' has been modified:
		Before:
			Biochemistry|process|http://edamontology.org/topic_3292
			Bioinformatics tools and formats||http://edamontology.org/topic_0091
			Chemical entity|material|http://purl.obolibrary.org/obo/CHEBI_24431
			Chemical structure||http://edamontology.org/data_1712
			Cheminformatics||http://edamontology.org/topic_2258
			Molecular Biology|None|http://edamontology.org/topic_3047
			Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367
			Molecular structure|information content entity|http://edamontology.org/data_0883
			lifescience|None|
		After:
			Biochemistry|process|http://edamontology.org/topic_3292
			Bioinformatics tools and formats||http://edamontology.org/topic_0091
			Chemical entity|material|http://purl.obolibrary.org/obo/CHEBI_24431
			Chemical structure||http://edamontology.org/data_1712
			Cheminformatics||http://edamontology.org/topic_2258
			Molecular Biology|None|http://edamontology.org/topic_3047
			Molecular entity|material|http://purl.obolibrary.org/obo/CHEBI_23367
			Molecular structure|information content entity|http://edamontology.org/data_0883
			Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069
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			Life Science|domain|http://www.fairsharing.org/ontology/SRAO_0000069
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			lifescience|None|

Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'The FAIRsharing Team' at 10:38, 19 Jul 2018 (approved):

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Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'MacroMol' at 17:09, 18 Jul 2018 (approved):

	'supportLinks' has been modified:
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			info@openHELM.org
			http://www.OpenHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
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			info@openHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
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			http://www.OpenHELM.org

Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'MacroMol' at 17:08, 18 Jul 2018 (approved):

	'supportLinks' has been modified:
		Before:
			info@openHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
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			info@openHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
			http://www.OpenHELM.org
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			http://www.OpenHELM.org
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Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'MacroMol' at 17:00, 18 Jul 2018 (approved):

	'tools' has been modified:
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			Webeditor
			HELM Antibody Editor 2
			HELM Toolkit
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			Webeditor
			HELM Antibody Editor 2
			HELM Toolkit
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Edits to 'https://fairsharing.org/FAIRsharing.pDq8lX' by 'MacroMol' at 16:48, 18 Jul 2018 (approved):

	'supportLinks' has been modified:
		Before:
			info@openHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://github.com/PistoiaHELM
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
		After:
			info@openHELM.org
			https://pistoiaalliance.atlassian.net/wiki/spaces/PUB/pages/8716303/HELM+Resources
			https://en.wikipedia.org/wiki/Hierarchical_editing_language_for_macromolecules
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			https://github.com/PistoiaHELM

In Collections

Chemistry

Support

General

support email	info@openHELM.org
online documentation	HELM Wiki
wikipedia	https://en.wikipedia.org/wiki/Hierarchic ...

Additional Information

Contact

info@openHELM.org

Tools

Webeditor	https://github.com/PistoiaHELM/HELMWebEditor	1.1.1
HELM Antibody Editor 2	https://github.com/PistoiaHELM/HELMAntibodyEditor2	1.0
HELM Toolkit	https://github.com/PistoiaHELM/HELM2NotationToolkit	1.3.4

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Database software

MIT Licence

Publications

HELM: a hierarchical notation language for complex biomolecule structure representation.

Zhang T,Li H,Xi H,Stanton RV,Rotstein SH
J Chem Inf Model 2012

View Paper (PubMed) View Publication

HELM Software for Biopolymers.

Milton J,Zhang T,Bellamy C,Swayze E,Hart C,Weisser M,Hecht S,Rotstein S
J Chem Inf Model 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Implementing Databases (1)

PubChem
PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links in the homepage.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by HELMInfo (MacroMol)

Maintains

Pistoia Alliance (Consortium)

Hierarchical Editing Language for Macromolecules

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