chemistry

Hierarchical editing language for macromolecules

Hierarchical editing language for macromolecules is a chemistry topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Hierarchical editing language for macromolecules rather than just read about it. In short: 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.

Key takeaways

Hierarchical editing language for macromolecules belongs to chemistry; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Hierarchical editing language for macromolecules to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Hierarchical editing language for macromolecules from memory before moving on to harder problems.

Reference excerpt

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. 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. The HELM open source project can be found on GitHub.

Background The need for a standard representation of biomolecules became apparent as researchers began working on modeling and computational projects involving molecules and engineered biomolecules. There was no language to accurately describe these entities, which required both composition and complex branching and structure. Protein sequences describe larger proteins, and mol files can represent simple peptides. However, the complexity of new research biomolecules makes describing large complex molecules difficult with chemical formats, and peptide formats are not sufficiently flexible to describe non-natural amino acids and other chemistries.

Design In HELM, molecules are represented at four levels in a hierarchy:

Complex polymer Simple polymer Monomer Atom Monomers are assigned short unique identifiers in internal HELM databases and can be represented by the identifier in strings. The approach is similar to that used in Simplified molecular-input line-entry system (SMILES). An exchangeable file format allows sharing of data between companies who have assigned different identifiers to monomers.

Examples

(For now, see the following external links: "HELM notation" on HELM wiki, and test data file.)

Adoption In 2014 ChEMBL announced plans to adopt HELM by 2014. The informatics company BIOVIA developed a modified Molfile format called the Self-Contained Sequence Representation (SCSR) A standard which can incorporate individual attempts to solve the problem and be used universally and avoid proliferating standards is a goal of HELM.

Tools An editor tool is needed to visualize and work with biomolecules at the correct level of detail. The editor is needed to "zoom out" to see a large molecule at the amino-acid sequence level, then "zoom in" to the atomic level at a particular site of conjugation or derivatization. The HELM Editor and HAbE (HELM Antibody Editor) are two client tools which may in the future be released as web-based applications.

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.

See also Simplified molecular-input line-entry system (SMILES) International Chemical Identifier (InChI) Molecular Query Language Molecule editor Chemical table file PLN protein line notation Molecular graphics FASTA

References

Worked examples

Example 1 — a first encounter with Hierarchical editing language for macromolecules

Start with the simplest possible case. Write down what Hierarchical editing language for macromolecules claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Hierarchical editing language for macromolecules before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Hierarchical editing language for macromolecules ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Hierarchical editing language for macromolecules

In research: Hierarchical editing language for macromolecules appears in chemistry research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Hierarchical editing language for macromolecules in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Hierarchical editing language for macromolecules is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, Chemical file formats, Chemical nomenclature, so understanding it makes those chapters shorter.
In everyday life: Look for Hierarchical editing language for macromolecules outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Hierarchical editing language for macromolecules in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Hierarchical editing language for macromolecules means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Hierarchical editing language for macromolecules out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Hierarchical editing language for macromolecules in simple terms?

Why does Hierarchical editing language for macromolecules matter?

Because it connects several chemistry ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Hierarchical editing language for macromolecules?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Hierarchical editing language for macromolecules.