HELM in Online Databases

HELM users have created and will continue to create content that are of use to other HELM adopters. These resources are not under the control of the project, but links to some of the more significant efforts will be posted here to aid the community.

PubMed

NCBI PubChem has gone live with it's new "biologic description" section, which includes HELM strings.

Example - a peptide HELM for oxytocin

https://pubchem.ncbi.nlm.nih.gov/compound/439302#section=Biologic-Description

EBI ChEMBL

The EBI has generated HELM notation  for just under 19K peptides that were previously associated with Mol files in the database and that contain at least three amino acids. This notation is available in the BIOTHERAPEUTICS table and also shown on the Compound Report Card. for example https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL1252

As a by product of this process the EBI has generated a list of more than 2 thousand monomers which are available as an XML file at

ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_20_monomer_library.xml