Monomer Aliases

A monomer is identified by its symbol, but chemists rarely agree on one name per residue. This article explains what an alias is, why the library lets one monomer answer to several names instead of storing duplicates, and the rules that keep every name unambiguous.

One structure, several names

Sarcosine is N-methylglycine. The public library registers it as meG, a peptide library imported from elsewhere calls it Sar, and a third team writes MeGly. Without aliases there are two bad options: register Sar as a second monomer with the same structure, which the duplicate check refuses and which would split every analysis in two, or rewrite every sequence to use meG.

An alias is a third option: an additional name for an existing monomer. Once Sar is an alias of meG, a HELM sequence written PEPTIDE1{T.[Sar].C} and one written PEPTIDE1{T.[meG].C} describe the same molecule, and the monomer appears once in the catalogue, under its symbol, with Sar listed in its Aliases column.

The symbol stays the monomer's identity. It is the name shown in the catalogue, the one the import uses as a key, and it cannot be changed. An alias is a name the monomer answers to; it can be added and removed at any time without touching the monomer itself.

Your aliases and public aliases

Aliases come in two scopes, like monomers:

• Your organisation's aliases are visible to your organisation only. You add and remove them, on your own monomers and on public ones alike: naming a public monomer your way does not copy it, and no other organisation sees your alias.
• Public aliases ship with the public library and are the same for every organisation. They are read-only, shown with a lock in the application, and change only with a service release.

The public aliases today are classic HELM spellings of public RNA monomers whose symbol differs by case only:

They are what lets the common notation RNA1{R(A)P.R(C)P} resolve against a library that registers ribose and phosphate as r and p.

One name, one monomer

Within a polymer type, symbols and aliases share one set of names. A name points to at most one monomer, across your symbols, your aliases, the public symbols and the public aliases. That is what makes a HELM sequence unambiguous, and it has a few consequences:

• An alias cannot be the symbol of another monomer, nor an alias already used by another one.
• A new monomer cannot take a symbol that is already an alias. R cannot become the symbol of a private RNA monomer, because it already names ribose.
• Names are case-sensitive. Sar and SAR are two different names, and only the one registered resolves. In HELM, case carries meaning: a is commonly D-alanine and A L-alanine, so the library never folds case for you. When a spelling such as SAR should work too, add it as an alias.
• The rule applies per polymer type. An alias of a PEPTIDE monomer means nothing in an RNA or CHEM polymer, and the same name can exist in two polymer types.
• An alias cannot contain /, which separates several aliases in a form field or an import cell, as in Sar/MeGly.

The full name of a monomer is a separate field with its own rule: it is unique within your organisation and the polymer type, but it is not a name HELM resolves.

When a name exists both in your organisation and in the public library, a situation the rules above prevent for new names but that older data can hold, the first match wins in this order: your symbol, your alias, a public symbol, a public alias.

What reads an alias

Everything that resolves a monomer from its name accepts an alias:

• HELM validation and conversion, used by Ideation and the structure editor. The output keeps the name as written: [Sar] stays [Sar] in the HELM returned, and a KET export carries a template named Sar. A sequence mixing meG and Sar keeps both spellings.
• The catalogue search on the Monomers page finds a monomer by any of its aliases.
• The service interface returns the monomer when it is asked for by an alias, always as its canonical record: real symbol, identifier and all the aliases you can see.

A FASTA file is the exception to case sensitivity. FASTA only encodes natural residues, one letter each, and conventionally uses lower case to mark regions, not different residues. It is read case-insensitively, and the HELM it produces is case-exact like any other.

The HELM services keep each organisation's monomer library in memory for up to five minutes. A new alias can therefore take up to five minutes to be accepted by HELM validation.

A known structure under a new name

The duplicate check refuses a monomer whose structure is already registered, by your organisation or in the public library, and the message names the existing monomer. When that refusal comes from a naming difference rather than from a mistake, the new symbol is exactly what an alias is for.

The bulk import can do this for you. With the option Register a known structure as an alias, a row whose structure is already registered does not fail: its symbol is added as an alias of the monomer that has the structure, no monomer is created, and the import summary lists those rows. Without the option, which is the default, such a row goes to the error file, so that a structure drawn without its stereochemistry is not silently filed under the wrong monomer. See Canonical SMILES and Duplicate Detection.

Aliases and history

Adding or removing an alias is not a material change: it does not create a version of the monomer and does not appear in the Version history. When a monomer is deleted, its aliases leave with it and are archived. A revive puts them back, unless one of the names has been taken by another monomer in the meantime, in which case the revive is refused and names the conflict. See Versioning and Deletion.

Who can change aliases

Every role sees the aliases. Adding and removing them needs the Manager or Administrator role, as for any other change to the library.

Related

• How to Manage Monomer Aliases
• Public Monomers
• Import File Format: the ALIASES column
• REST API: the alias endpoints