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ChemAxon provides various conversion utilities from and to HELM within their Biomolecule Toolkit for peptide- and nucleic acid-derived molecules . (https://www.chemaxon.com/products/biomolecule-toolkit/)
Supported file formats for exporting include XHELM, FASTA, plain sequences and MDL/Mol files*. Sequences from HELM are generated using the Natural Analogue information of HELM monomers. Mol files will be exported in v3000 format containing S-group abbreviations for each monomer.
Supported file formats for importing include FASTA, plain sequences and MDL/Mol files*. FASTA headers are maintained in the HELM annotation section. Import of Mol files is currently limited to molecules, which are fully represented by a given monomer dictionary. This dictionary may be a fully custom/proprietary one.
Until mid 2016 import of PDB files is expected to become available.
*Other chemical file formats can be converted to MDL Mol-file representation using ChemAxon's Molconvert.
Biovia Pipeline Pilot
Biovia's Pipeline Pilot contains HELM reader and writer components in its chemistry collection. It does not fragment atom/bond representations but can convert sequence-based notations. There is HELM support in some other Biovia tools - see the PDF below for details.
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