Dotmatics RNA Therapies Solution

Driving Innovation for Novel RNA-Based Therapeutics

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Cutting-edge science requires cutting-edge tools

RNA therapies come in various forms, acting to either up-regulate or down-regulate protein translation to solve disease conditions. Successful development of RNA-based therapeutic candidates requires the interplay of chemistry and biology. Chemical modifications are crucial to ensure efficacy and to protect the therapies from rapid degradation. Discovery project teams are cross-functional, drawing on the skills of chemists and biologists alike. Data management systems for RNA therapies research must also provide cross-functional capabilities and be adept at handling the complex science involved.


Cross-Functional Informatics Solutions for RNA Therapeutics

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Can you...

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Find and view project data how you want to, as a chemist or biologist?

RNA therapies are at the leading edge of scientific innovation, driving the latest advancements in chemical modification of biological sequences. Cross-functional teams of biologists and chemists need to search to, and view, a single source of scientific truth but through distinct lenses that match their scientific understanding. Chemists will mostly perform structure searches, biologists will use sequence searches. Either could represent a functionally equivalent query, and therefore find the same results.

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Accurately define and protect your scientific innovations?

RNA therapies research is extending scientific boundaries at a rapid rate. It’s critical that you can fully and accurately define your candidate therapeutics, so you know exactly what you’re working with, and you can establish intellectual property protections.

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Capture your scientific data?

In order to be able to view your data, you must first capture it. And not just capture in any way. It must be captured  in a way that meets the joint goals of not getting in the way of science, but also ensures the data is of the highest quality and accuracy, and can be found again by anyone who needs to.


With Dotmatics you can

icon Work collaboratively in cross-functional teams, sharing data and viewing it as you want

RNA therapy development requires close coordination between chemists and biologists. Understanding how chemical modifications affect the structure and mode-of-action of RNA molecules is critical to developing effective candidates. It’s crucial that data management systems inherently understand both chemistry and biology, that they store a single representation of therapeutic candidates. To find that data, users must be able to query in their natural “scientific language”–structures for chemists, and sequences for biologists, and and view the results accordingly. This allows cross-functional teams to communicate and collaborate effectively, on high quality data. The Dotmatics Platform, along with its end-user modules, is the only enterprise-scale informatics system that can meet these requirements. Whether you are a start-up, or a multinational biopharma organization, you still need enterprise-scale tools to achieve your corporate objectives.

icon Register full chemical details of your RNA therapies to define uniqueness and protect your intellectual property

A critical component of the Dotmatics solution for RNA Therapies development 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 conjugated RNAs. Collectively, these capabilities ensure that you know exactly what your candidates are, and you can fully protect your intellectual property (IP).

icon Capture research data simply, but in a way that allows you and colleagues to find it at any time

The Dotmatics solution for RNA therapy development 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. Experiment templates in the Dotmatics ELN, Studies Notebook, are configurable and can range from simple, “paper-on-glass” protocols used for exploratory experiment, through to high-structured protocols that follow formalized procedures. Studies Notebook templates can be configured to support chemistry or biology-based workflows. In all cases, data are captured, indexed and made available to authorized personnel as soon as possible. This is a hallmark of Dotmatics — to ensure data are findable and usable, not locked away in silos.

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 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 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 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

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