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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.
Certara:
Certara’s D360 application for scientific informatics supports discovery research scientists through self-service access data access, integrated analysis and data visualization capabilities combined with collaboration tools to improve data driven decision making. D360 has been deployed in support of small molecule and research into other modalities such as antibodies, ADCs, oligonucleotides, and peptides. D360 supports the use of HELM notation for searching, filtering and rendering other modalities. More advanced functionality, such as sequence formatting, alignment and clustering based on HELM representation allows users to determine and exploit sequence-activity relationships.
ChemAxon:
Biomolecule Toolkit and the macromolecule sketcher BioEddie are natively supporting the HELM standard. The tools provide capabilities for managing a centralized monomer library, registering and performing uniqueness checks of macromolecules, generating a HELM notation from small molecule representations and sequences, and representing modalities with partially or fully unknown chemical structures.
Roland Knispel, Project Lead for Biologics Informatics at ChemAxon, said, “Our HELM-based tools are helping our customers to manage chemically modified sequence-based modalities. A single environment for various types of modalities, improved data quality and utilizing an industry-wide standard for data exchange are the key benefits reported back to us by our users. By market demand our platform is now being integrated into solutions provided by IDBS and other partners.”
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