HELM Phase 1 Exceeded Expectations

The Pistoia Alliance HELM project started almost two years ago in December 2012 when David Klatte proposed that the Pistoia Alliance help open source a technology first developed for internal use at Pfizer. That technology was HELM and it enabled the representation of complex macromolecules. The Pistoia Alliance membership enthusiastically embraced the idea and the HELM project was born.

The first phase of HELM had the following objectives:

  • Make the internal Pfizer code independent of internal Pfizer systems and making it available to the wider community free of charge.
  • Set up a community to govern the standard and manage enhancements and further development work.
  • Promote the standard and encourage adoption.

Although the original project plan scheduled the code to be available in Q4 2013, the project exceeded all expectations and released the code well ahead of schedule in May 2013, having only used a small fraction of the original budget. Particular thanks go to ChemAxon who provided the development resource, and Sergio Rotstein (Pfizer) who took over from David as project lead, but it was the time, expertise and effort from a very large number of companies which enabled such a lot of work to be completed in a short period of time.

Instead of closing the project at this stage the steering committee decided to continue and use the remaining funds to extend HELM and continue to encourage adoption. Further technical developments ensued:

  • xHELM – an exchangeable format that includes monomer definitions in the notation.
  • Search prototype from Cambridge University.

In parallel, others got involved:

  • EBI started converting ChEMBL structures to HELM format.
  • Roche extended the HELM editor to recognise and display antibody domains.

And at the time of writing we have a growing list of companies who are using HELM, have active projects to use HELM or are involved with the project and have supplied funds:

  • Vendors: ChemAxon, Biovia, BioMax, Next Move, Sciligence, BioChemFusion, Arxspan, eMolecules, ACD Labs
  • Pharma: BMS, GSK, Lundbeck, Merck, Novartis, Pfizer, Roche

Just to encourage the team even more, we won a BioIT World Best Practices Award for 2014!

Our heartfelt thanks go to the many people and organisations who contributed to the project. We have thoroughly enjoyed working with you and appreciate everything you have done.

Having achieved far more than we expected, the initial phase of HELM is at a close, but such a successful standard does not and should not stand still. The new project OpenHELM intends to build on the foundations and address key extensions identified by HELM adopters. There is more to come and we look forward to an exciting future.

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