Munich, October 14th, 2015 – The Pistoia Alliance, a global alliance of life science companies, vendors, publishers, and academic groups, has selected quattro research GmbH to implement the HELM 2.0 project (“Ambiguous HELM”). This initiative will enable HELM to represent biomolecules in which some aspects of the structural composition or assembly are not fully determined.

Scientists have struggled to represent non-standard biomolecules in their systems leading to “pick and mix” approach of multiple nomenclatures and textual descriptions. HELM, the open standard, enables the representation of multiple types of complex macromolecules including nucleotides, proteins, antibodies and drug-antibody conjugates including ones containing non-natural elements.

Created by a team at Pfizer, the Pistoia Alliance formalized the HELM notation as an open standard in early 2013 and publicly released software tools to the Open Source community. Since its release, HELM has benefited from a growing range of global adopters and contributors, which includes ACD Labs, Arxspan, Biomax, Biovia, BMS, ChemAxon, EMBL-EBI, eMolecules, GSK, Lundbeck, Merck, NextMove, Novartis, Pfizer, quattro research, Roche, and Scilligence.

While the existing HELM approach solves the problem of representing unnatural complex biomolecules, it still assumes that the scientist knows everything about the structure. In biology this is rarely the case, with the outcome of experiments subject to a number of uncertainties. Currently scientists have a difficult choice: either imply they have all the information and guess at a structure, or record a textual description and put no structural information in their corporate databases. Ambiguous HELM allows the structural information that is available to be captured in a useful way, while also identifying what is not known.

The HELM 2.0 project aims to implement a number of enhancements to the current HELM definition and open source codebase:

  1. Extend the HELM notation and the HELM toolkit to allow for the representation of ambiguous macromolecules.
  2. Create an API which allows the toolkit to access different chemical libraries.
  3. Create web-services for the toolkit to abstract the toolkit functionality from the code implementation.

“HELM has already delivered a practical way for researchers to represent complex biomolecules computationally. Through our partnership with quattro research, HELM will now be able to gracefully deal with the all-too-common situation of entities with uncertain or ambiguous structural features, an important expansion in the usability – and consequently – the adoptability of the technology” said Sergio Rotstein, Director of Research Business Technology at Pfizer and Domain Lead for the Pistoia Alliance HELM initiative, comment.

Markus Weisser, Managing Director at quattro research GmbH added: “HELM is designed as an open source project. Hence, it is important that we now start to remove third party dependencies and provide a more service-oriented architecture. This will lower the barriers to contributing to the development of HELM and attract even more companies to join the HELM community. During the last one and a half years, quattro research has become a leading expert in HELM and its extensions. We have helped to develop the extension xHELM and contributed to the development of the HELM Antibody Editor. We are very proud that the Pistoia Alliance has chosen us to implement HELM 2.0 and look forward to another successful collaboration.”

About the Pistoia Alliance:

The Pistoia Alliance is a global, not-for-profit alliance of life science companies, vendors, publishers, and academic groups that work together to lower barriers to innovation in R&D. Our projects transform R&D innovation through pre-competitive collaboration. We bring together the key constituents to identify the root causes that lead to R&D inefficiencies. We develop best practices and technology pilots to overcome common obstacles. Our members collaborate as equals on open projects that generate significant value for the worldwide life sciences community.

About quattro research GmbH:

quattro research GmbH is a software and service company located in Munich, Germany. quattro research offers services and products for data management in the pharmaceutical, chemical, and biotech industry. The primary focus of the company is the development of tools and services for compound registration and analysis of biological data. Within several projects, quattro research developed extensive knowledge in the management and registration of biologics, e.g. antibodies and peptides. For further information see or email

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