HELM Reference Implementation

The HELM project has created a number of tools that are available for free. These illustrate the capabilities of HELM and can be adapted to your organisation.

HELM Editor

Create and visualise HELM structures. Convert and edit exiting sequences. Manage monomers and annotate RNA strands.

HELM Toolkit

The HELM toolkit is the foundation of everything. It provides the core functionality that other tools use. Available on GitHub, with Java doc guide to the functionality.

HELM Antibody Editor (HAbE)

Analyse your antibody sequence information. Automatically recognise domains, identify domain origins, automatically create Cys-Cys links, manually edit them and more...

HELM Searching

In 2014 a Cambridge University summer student developed a search proof of concept. Contains substructure and subsequence search functionality, and combinations. Available for those who want to include searching in their own application.

External Information and Monomer Set

An initial monomer set of several thousand amino acids available as an xml file. Created as part of a collaboration between the EBI and the Pistoia Alliance. HELM notation is also available in ChEMBL 20.

Contact Us

Ask us questions, send comments, get in touch. We love to support HELM adopters.


Links to the HELM code, user guides, videos, specifications and more can be found on our wiki.