BioIT World has written a really good article about HELM. Please take a look…
As a taster, here’s an excerpt:
HELM addresses a problem at the root level of drug discovery. Pharmaceutical and biotech companies are looking at increasingly complex molecules in the search for new therapeutics, testing out RNA- and peptide-based compounds that tap directly into cellular pathways. The trouble is that these large molecules, which are often hybrids of RNA, amino acids and other chemical structures, are difficult to concisely describe, even when their structures are perfectly known. They are too large and ungainly to represent atom-by-atom, but not uniform enough to be reduced to nucleotides and peptide chains.
“There have been a number of ways to represent small molecules,” says Rotstein. “That’s been the bread and butter of a number of companies for a long time, and that’s the realm of cheminformatics. And there’s been a lot of methodology for dealing with sequence-based entities, like genes and proteins, which is the realm of bioinformatics. The issue is that the types of molecules that we are targeting fall in between these two.”