The Pistoia Alliance and EMBL-EBI Announce HELM Collaboration for Cheminformatics

Cambridge, United Kingdom, February 4, 2014 – EMBL-EBI is collaborating with the Pistoia Alliance, a precompetitive leader in the life-sciences industry, to help improve data resources for the study of pharmaceutically relevant molecules. During 2014 ChEMBL, EMBL-EBI’s database of bioactive entities with over a million compounds will incorporate the Hierarchical Editing Language for Macromolecules (HELM) notation, a Pistoia Alliance-led standard in biomolecular informatics.

Bioinformatics and cheminformatics have rapidly advanced in the past five years thanks to the steady increase in publicly shared data and chemistry software tools. But as the development of new classes of drugs has increased, so has the demand for standard informatics methodologies that can be used to study larger, more complex molecules.

HELM can be used to represent simple macromolecules like oligonucleotides, peptides and antibodies. But it goes a step further by enabling the representation of very complex entities such as those with unnatural amino acids, or conjugated species such as antibody-drug conjugates. ChEMBL, a comprehensive repository of bioactive drug-like molecule information, covers over a million compounds with 12 million associated bioassay measurements on nearly 10,000 targets. Incorporating the HELM standard into ChEMBL’s data pertaining to peptide-derived drugs and compounds will provide pharmaceutical researchers with the means to query this data in new ways.

Sergio Rotstein, Director of Research Business Technology at Pfizer, is the HELM project lead for the Pistoia Alliance. He stated, “The integration of HELM into ChEMBL represents a significant step forward in facilitating the exchange of bio-molecular information within the life-sciences R&D ecosystem. We are thrilled to see a key institute like the EBI joining the growing list of HELM adopters.”

John Overington, Head of Chemogenomics and Molecular Systems Resources at EMBL-EBI, articulated, “We are pleased to be among the first content providers to incorporate this innovative macromolecular information standard, and hope this will lead to the development of value-creating tools for researchers working in protein engineering and drug design.”

John Wise, Executive Director of the Pistoia Alliance also stated, “It is very rewarding that the EBI, a member of the Pistoia Alliance, has recognised the importance of this emerging standard and is demonstrating such a strong commitment to it.”

HELM will be incorporated into the ChEMBL content for peptide-derived drugs and compounds in version 20.

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