Dotmatics Chemically-Modified Therapeutics Solution

Bridging Biology and Chemistry for Novel Therapeutics

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New science drives critical data management needs

A rapidly emerging trend in drug discovery is the development of chemically-modified therapeutics. These are biologically-based molecules that contain some form of artificial chemical modification. These therapeutics can access new areas of pharmacological space, or access known pharmacological space more effectively. A second motivation is to avoid some of the challenges of conventional biologic therapeutics. These include dosing methodologies, effective targeting, pharmacokinetics and immunogenicity.

Can you...

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Capture all the data that supports your science?

Development of chemically-modified therapeutics requires an understanding of both chemistry and biology. Cross functional teams need a variety of ad hoc and standardized workflows to effectively capture all project data.

Track and view all of your data, at any time?

Chemically-modified therapeutics discovery projects generate large volumes of diverse data. This creates challenges in managing the data, especially tracking relationships between candidates. Viewing all project data in context is critical for informed decision-making.

Protect your scientific innovations?

Competition in the bio-pharma industry is fierce. Many companies are targeting the same therapeutic areas. Scientific innovation in novel therapeutics design and experimental processes are valuable assets. They need rigorous protection.


With Dotmatics you can

icon Embrace a diverse set of therapies

Included in this definition are antibody-drug conjugates (ADCs), peptide-drug conjugates (PDCs), antisense oligonucleotides (asRNA), small interfering RNA (siRNA), modified RNA (modRNA), stapled peptides, and cyclic and bicyclic peptides. This is clearly a diverse set of molecules, varying greatly in size and composition, but the common feature of being chemically-modified creates significant challenges for most scientific informatics systems. These systems are built to handle either chemistry or biology data, but rarely can they manage both. This causes significant barriers for the cross-functional teams that typically work on developing these novel therapeutics.

icon Manage both chemistry and biology project data in a single system

Systems that support only chemistry or biology can’t capture the full scientific definition and information for chemically-modified therapeutics, undermining this research and weakening intellectual property (IP) protections. Collaborations between chemists and biologists are hindered, slowing project progress. In some cases, organizations will adopt two informatics systems, one for biology data and one for chemistry data. This is also sub-optimal because the fidelity of the entity definitions across the systems cannot be guaranteed. Data integration becomes difficult, again undermining IP protections, data quality and cross-functional team collaboration.

icon Capture the full detail of chemically-modified therapeutics across your enterprise

The Dotmatics solution for chemically-modified therapeutics provides the scientific rigor needed to completely capture the full detail of these entities and delivers the broad set of informatics capabilities to fully support your project goals. The Dotmatics Platform inherently understands both chemistry and biology, to ensure that project data is captured and managed by a single source of truth. This ensures that IP protection is maintained, data quality is at its highest, and cross-functional teams of scientists can collaborate efficiently and effectively.

icon Register chemical uniqueness of biomolecules to protect your IP

The core of the Dotmatics solution for chemically-modified therapeutics is Bioregister, our biological registration system that generates a full chemical representation of sequence-based entities, using InChI keys. Users can easily transition between sequence and molecular views, or simply use whatever makes most sense to them, as a chemist or a biologist. The full chemical representation is used for uniqueness checking, and chemistry-based searching can be performed. Bioregister also generates HELM notations for these entities, which is often useful for communicating with strategic partners. Bioregister can create implicit bioconjugation linkages based on “click chemistry”, to streamline the definition and capture of ADCs and PDCs.

icon Support novel therapeutics research for biologists and chemists

Supporting Bioregister, Dotmatics provides many other modules as part of the Platform. Studies Notebook, the Dotmatics Electronic Lab Notebook (ELN) is build to be flexible, allowing templates to be configured to support chemistry or biology-based workflows. If you’re doing more investigational experiments, those are supported too with a simple Discovery ELN template. Vortex, our advanced analysis and visualization application includes advanced algorithms for chemistry and biology analyses, and can display chemically modified therapeutics in either molecular or sequence format. And ultimately, Dotmatics Browser is the key tool allowing scientists of all types to search, browse and view their data, and make well-informed decisions that accelerate their research and innovation.


This solution consists of

iconDotmatics Browser

Dotmatics Browser is a powerful web-based search and reporting solution that provides federated searching across Dotmatics and third party research databases, enabling research scientists to access all of their data whenever they need it, irrespective of where it is stored.

  • Integrates chemical, biological, assay, notebook and other research databases to provide a single federated search and browse capability
  • Provides scientific search, such as chemical substructure and similarity
  • Manages project level and personal search forms and views, queries, lists and reports
  • Powerful scientific data visualization as forms, tables and charts.

iconDotmatics Studies Notebook

Dotmatics Studies Notebook is an Electronic Laboratory Notebook (ELN) with flexible templating to capture, store and search experiments from all scientific disciplines.

  • Dotmatics Studies Notebook allows scientists to capture and store their experiments in a form that is easily searchable by all team members. It allows organizations to secure and audit IP and define signing workflows
  • Flexible protocols (implemented as templates) allow the single ELN to accommodate highly structured experiments such as synthetic chemistry and protein purifications, as well as more ad hoc experiment types often useful for target identification and discovery biology experiments. Ad hoc experiments are also often used to support a transition from paper based notebooks
  • Dotmatics Studies Notebook allows for collaboration on experiments by multiple scientists within or between organizations

iconDotmatics Bioregister

Dotmatics’ Bioregister is a web-based application for registering sequence-based, chemically-modified and structureless biological entities, allowing biologics discovery organizations to ensure entity uniqueness and protect their intellectual property. Bioregister supports management of a broad set of biologics entities, including DNA, RNA, peptides and proteins, antibodies, conjugates, non-natural peptides and nucleotides,  plasmids, cell lines and user-defined entities. It also enables users to record batches and samples for these entities, purification and expression information, and other protein production data.

  • Records and manages biologic entities, including chemically-modified sequences and sequence-less entities, and associated attribute data and lineages
  • Generates chemical representation (where possible) of natural and non-natural entities
  • Determines the uniqueness of entities and assigns registration numbers, including using full chemical-based uniqueness where possible
  • Manages data associated with entity production, such as protein expression, purification and characterization
  • Records batches and samples of protein produced for the entities, with full relationship tracking

iconDotmatics Vortex

Dotmatics Vortex is an interactive data visualization and analysis solution for scientific decision support. Building on and extending the spreadsheet paradigm, it provides the data manipulation, statistical analysis and sophisticated plotting capabilities required to explore and understand any complexity and size of data. Vortex is also scientifically aware providing native cheminformatics and bioinformatics analysis and visualizations.

  • Allows users to understand, refine and select from large and/or complex data sets
  • Allows teams to collaborate on scientific analysis through shareable workspaces and reusable templates
  • Understands numeric, textual, image, chemical structure and biologic sequence data
  • Generates high performance, interactive visualizations, including charts and tables
  • Handles very large datasets – e.g. tables of millions of compounds by thousands of descriptors or cells containing whole genome sequences
  • Has inbuilt data mining, statistical, cheminformatics and bioinformatics analysis functions
  • Loads data from many types of file or when used in conjunction with Browser, directly from databases

iconDotmatics Studies

Dotmatics Studies is a highly flexible, innovative screening data management solution to capture and analyze all types of screening experiments from high content (HCS) and high throughput (HTS) to dose-response and DMPK studies.

  • Defines analysis protocols for plate and non-plate based assays
  • Provides out-of-the-box and custom assay protocols, curve fit calculations, plate readers, and plate layouts captured and stored for re-use
  • Supports very high data volume assays
  • Defines business rules for very automated classification of results
  • Manual or automated processing allows screening scientists to apply the screening protocols to process raw instrument and validate the results, or experiment creation and processing to be driven via an automation layer.
  • Once completed and validated, screening results are immediately available via Browser to the project team

iconDotmatics Platform

The Dotmatics Platform is the common framework that supports the Dotmatics web-based scientific applications and allows them to work together to provide users seamless end-to-end workflows. The Platform supports managed deployments in the Cloud or self-supported deployments on premise. An open architecture enables workflows to include third-party software integration. When used together with Dotmatics Browser the Platform allows federated data access across corporate and external research data.The Dotmatics Platform is completely unified – it provides common data models, code and architecture to support business workflows that span the capabilities of the individual applications. This is important for enterprise enablement of research organizations, providing ease of maintenance and development. It gives the lowest possible total cost of ownership compared to platforms that support their applications with less tightly integrated collections of multiple technologies and/or architectures with multiple development histories.

  • Provides the framework that supports all Dotmatics web-based scientific applications and allows them to work together to provide seamless workflows.
  • Portal for administrators to manage users and groups, applications and configurations
  • Provides APIs for automation and integration with 3rd party software
  • When used in conjunction with Dotmatics Browser provide access to data from across an organization and externally

iconDotmatics Inventory

Dotmatics Inventory is a fully searchable sample and materials inventory that tracks chemicals, biologics, instruments and associated data across a hierarchy of locations and manages the dispensing and plating workflows, as samples are moved through an R&D process.

  • Defines a hierarchy of storage locations for an organization
  • Track samples in containers such as bottles and plates in those storage locations
  • Manages research materials, reagents and assets
  • Manages the aliquoting and dispensing workflows to distribute samples for testing
  • Maintains a full audit trail
  • Allows for searching and reporting on inventory information alongside other corporate data

iconDotmatics Cascade

Dotmatics Cascade manages the requesting and assignment of laboratory tasks, and tracking the progression of samples, across multiple teams within an organization or across a collaborating network.

  • Dotmatics Cascade allows organizations to define available services, such as assay execution or analysis and the associated scientific team
  • Scientists create requests for services and submit compounds Service managers manage, group and assign requests for execution
  • Service team scientists accept requests, create and autopopulate experiments to execute them
  • Teams can see request status and monitor compound or sample progression