Informatics Tools leveraging the open HELM standard for managing and exploring databases of chemically modified complex biomolecules
ChemAxon's novel Biomolecule Toolkit is bringing the HELM standard to life. The ChEMBL v21DB contains ~ 20000 peptides published in both MOL and HELM format, which we used as a benchmark for measuring the ability of our tool to start from a set of chemical representations, convert it to HELM, and index it in a database. Finally we performed queries on the indexed content, which were not possible previously using the default ChEMBL web interface. Along the way we encountered a few challenges and data issues, of which a select few are detailed below. Our tool provides a solution for these and may help to improve ChEMBL and other datasets.