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ACD/Labs supports HELM across our portfolio, from the ACD/Labs Biosequence tool (ACD/ChemSketch) to our array of software for analytical chemistry ACD/Spectrus, and the Luminata CMC project decision support application, to the recently announced Katalyst D2D for high throughput and parallel experimentation. Notations for biomolecules ranging from small peptides to whole antibodies can be imported from HELM and xHELM files and exported in HELM file format. “HELM notation is the cornerstone of our expanded molecular characterization efforts, from small molecule to biologics”,- says CEO Daria Thorp.


Benchling supports chemically modified oligonucleotide design, analysis, and characterization in a high-throughput manner using HELM notation. By standardizing on HELM in a single platform, R&D teams can centralize experimental results, standardize oligo sequences and naming uniqueness during registration, and collaborate with teammates more effectively. HELM allows scientists using Benchling to establish a scalable common language across organizations, improve data quality, surface real-time scientific insights, and accelerate the speed of the full therapeutic lifecycle. Benchling users can also interconvert ITD syntax to HELM sequences making it easier to share designed sequences with vendors and collaborators.


Applications use Biovia’s proprietary SCSR (Self-Contained Sequence representation, an extension of the V3000 molfile) format, but there is extensive ability to import, export and convert to and from HELM. Pipeline Pilot Chemistry Collection contains importers and exporters, HELM readers and writers including XHELM, and components to interconvert between macromolecules represented by HELM, full chemistry and SCSR. HELM support is available in Insight, the Draw and Pipette sketchers, biological registration and the chemistry cartridge.