Biopolymer Informatics

Merging chemistry and biomolecules

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Your Challenge

An increasing number of new FDA approved drugs are biologics; in 2017 alone, a quarter of the novel drug approvals were biological entities. Despite the growth in biologics research there has not been a parallel growth from the informatics side. The cheminformatics world is well versed in terms of software to draw, store, search, report and manage small molecules. However small-molecule technologies are not suited for representing large biomolecular entities. And while bioinformatics has provided sequence-based technologies for many years, these fail to represent biomolecular modalities that include modifications such as unnatural amino acids and nucleotides, post-translational modifications, and other chemical modifications (e.g. bioconjugates).

Our Solution

ChemAxon has aimed to remedy the informatics gap between small and macromolecules by introducing its biomolecule technology. Our aim is to come up with the equivalent of our existing chemical software portfolio for the world of Biologics.

Draw and visualize macromolecules

The base of our bioinformatics technology is an intuitive, fully web-based sketching tool for defining and visualizing a diverse set of biomolecules such as peptides, oligonucleotides, proteins, antibodies, and antibody-drug conjugates, including those containing unnatural, chemically-modified, and non-structure components (e.g. nanoparticles). Any of the above may be represented with full, partial or no chemical structure information and added annotations. Our solution offers native support for sequence, HELM and MOL file interconversion, allowing seamless transition from sequence to molecular structure and the way around. With a simple API, it is easily integrated with existing web-enabled software tools.

BioEddie - representing biomolecules on atomic level
Connecting chemistry and biology

Register, store and search biologics

Our technology provides unambiguous representation of biomolecules at the sequence and atomic level, thereby enabling standardization, registration and search of biologics and associated data within a database. The toolkit may be accessed through Rest Web services or the JAVA API to extend existing biologics management platforms or to form the basis of a biomolecule registration system. The provided search service enables you to build complex queries against the registration database, supporting combinations of sequence filters (e.g. subsequence search) and chemical structure filters (e.g. substructure search) to identify all relevant hits. Additional services can perform property calculations of your biomolecules or interconvert between popular file formats (MOL/FASTA/HELM).

Success Stories

Macromolecules in E-Workbook with Marvin JS and BioEddie

Biological macromolecules play an important part in a modern pharmaceutical pipeline, given the rising interest in th...

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Roland Knispel (ChemAxon) & Conor Scully (Heptares): HELM-Driven Tools for Peptide-based Drug Design

The HELM (Hierarchical Editing Language for Macromolecules) standard is rapidly gaining wide acceptance in industry a...

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Meeting the ever-changing demands of synthetic chemistry

The in-silico tools and resources for a Design-Make-Test paradigm in small molecule chemistry have significantly adva...

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What about the "big guys"? The emerging HELM standard for macromolecular representation and the Pistoia Alliance

The recent increase in utilization of complex macromolecules such as Antibody-Drug Conjugates (ADCs) as therapeutic a...

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Draw & visualize biomolecules on web

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Biomolecule Toolkit

Back-end for connecting biology and chemistry

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Get Connected with ChemAxon

Our solutions can be integrated into a wide variety of software environment, with thousands of features supporting scientists. We can help find the best combination for your R&D.

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