Biomolecule Toolkitnew

Bridging chemistry and biomolecules

ChemAxon’s Biomolecule Toolkit is a webservice-based toolkit to bridge the gap between biology and chemistry for complex biomolecular entities. It provides unambiguous representation at sequence and atomic level for a diverse set of biomolecules such as peptides, oligonucleotides, proteins, antibody drug conjugates, including those containing unnatural and chemically-modified components, thereby allowing their storage, indexing and search within a database.

The toolkit can be applied to extend existing biologics management platforms or to form the basis of a biomolecule registration system. It is capable of mapping your specific workflows and business logic for canonicalization, registration and querying.

Product Type:application
Interfaces:GUI ( Web )API ( Web )

Application areas

Peptide-based therapeutics

Most native peptide sequences are rapidly eliminated post administration, hence suitable candidates are often either chemically modified within the sequence, or conjugated to chemical components with the aim to reduce degradation or renal clearance.

The Biomolecule toolkit facilitates unambiguous representation and registration of linear and cyclic peptides.

Containing natural and synthetic amino acids, chemical modifications and conjugates; the toolkit maintains a searchable catalogue of peptides. We are working towards providing tools to create focused virtual libraries by enumerating sequences via targeted residue replacements with natural or unnatural amino acids and subsequent property-based filtering to aid in quickly expanding structural diversity based on a given lead sequence.

Peptide-based therapeutics

Antibodies and Antibody drug conjugates

Antibodies and Antibody drug conjugates

Various antibody and antibody drug conjugate formats exist, currently but in most cases they cannot be described precisely at the atomic level. A unique representation of these molecular entities can only be realized by incorporating additional numerical or textual annotations of either parts of the molecule or the entire entity, typically in the form of attribute-value-pairs (i.e. antibody drug ratio – ADR for antibody conjugates), in addition to exact (i.e. sequence of antibody chain), and fuzzy (i.e. conjugation sites of a given payload) structural features.

The Biomolecule toolkit includes a functional layer to define, store and query annotations and make them available when defining the business logic for registering and searching unique complex biological entities within a database. Our data model for storing annotations is a precursor for more robust support of macromolecule components, which cannot be meaningfully defined by a chemical structure, i.e. quantum dots, dyes or other diagnostic markers, but rather rely on describing e.g. particle size, mode of action etc. as attribute-value-pairs.

RNAi-based therapeutics

Antisense oligonucleotides and small interfering RNAs are typically short (12-22 residues) stretches of nucleic acid that hybridize to their complementary RNA substrate sequences, thereby inactivating the substrate by reducing free substrate concentration below an effector concentration threshold, or by inducing ribonuclease H1 degradation of the formed RNA/DNA duplex.

As peptides, antisense oligonucleotides are prone to quick degradation, which can be countered by incorporation of chemical modifications to the nucleic acid backbone, e.g. methoxyethylation on the 2’ position of the ribose component. Using the Biomolecule toolkit, such chemically modified oligonucleotides can be easily created, stored and indexed in a canonical form.

Sequence-based assessment of your RNA candidate molecules can then still be available to your favorite bioinformatic tools, while the chemical features of your molecules are preserved.

RNAi-based therapeutics

Agnostic registration

Development of novel therapeutic entities is largely driven by the identification and validation of biological targets for a specific condition, followed by a search for therapeutic candidate entities, which can be small molecules as well as Biologics, modulating this target in a favorable manner.

The Biomolecule toolkit provides out-of-the-box functionality for handling and registration of complex biomolecules and associated data which can be readily integrated into applications.

Current works are toward an integrated platform, which can accommodate novel chemical and biological entity management side by side in a type-agnostic system, which serves as a single point of reference for your therapeutical candidate entity inventory.

A key component of the registration solution is a perception engine, which interprets a submitted entity, independent of its submission format, and feeds this through the internal business logic to the registration database.

This requires the ability to seamlessly round trip between different representation formats in which the submitted entities might arrive.

Agnostic registration


The Biomolecule toolkit provides JChem-like functionality within a Web Service API framework for complex biomolecules, which are notoriously difficult to handle using classical chemoinformatic and bioinformatic tools. The toolkit provides SOAP and REST-ful APIs to make deploying within existing IT infrastructures straightforward and flexible.

Biomolecules and associated data are held in a relational database alongside the chemical structures of any constituents, e.g. amino acids, in JChem tables. Access to this database for registration of new entities, updates to existing entities, deletion of obsolete content is managed by the Web Service API.

The 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 perform property calculations of your biomolecules or interconvert between popular file formats (e.g. HELM, FASTA, MDL Mol v3000).


Articles in the library

Biomolecule Toolkit

May 24, 2016 - Presentation
ChemAxon’s Biomolecule Toolkit is a webservice-based toolkit to bridge the gap between biology and chemistry for complex biomolecular entities. It provides unambiguous representation at…

Biomolecules at ChemAxon

Sep 14, 2016 - Presentation
ChemAxon’s Biomolecule Toolkit – now extended with an editor, called BioEddie – is a webservice-based toolkit to bridge the gap between biology and chemistry for complex biomole…

What about the “big guys”? The emerging HELM standard for macromolecular…

May 29, 2013 - Presentation
The recent increase in utilization of complex macromolecules such as Antibody-Drug Conjugates (ADCs) as therapeutic agents has revealed a substantial gap in the biopharmaceutical industry…

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