Dotmatics Solutions for Life Sciences Research

Maximizing lab efficiency and driving informed decisions

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Enhancing efficiency and supporting innovation

Life sciences research is multidisciplinary, multi-modal, data-centric and characterized by ever-evolving scientific methods. Your research informatics solution must be able to keep up.

It should:

  • Support workflows of research teams racing to discover new therapeutics; and do this for an ever-increasing range of therapeutic entities.
  • Optimize efficiency whether research is conducted across a team in a single lab or multiple teams working in a multi-company, collaborative network.
  • Be able to adapt to the volume and diversity of today’s research data, and to the increasing automation that is driving the lab of the future.
Your challenges

Can you ...

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Capture all your science?

Life science researchers are expanding the breadth of therapeutic types. These range from small molecules to natural and chemically-modified biologics, and cell and gene therapies. All these entities, and the vast array of data associated with them, must be captured within laboratory informatics systems. Crucially, those systems must allow the data to be searched and analyzed in decision support systems.


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Collaborate effectively?

A discovery project crosses departments, scientific disciplines, physical locations and often companies. Requests, data and results need to flow seamlessly between all members to ensure the efficient execution of the project.

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Make fully informed decisions?

Every member of the project team needs real-time access to project data. They should see all the data for which they have permission, at any time, and irrespective of where it is stored. This ensures that they can make the best-informed decisions about project progression.
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Maximize your efficiency?

Increasing efficiency will reduce discovery cycle times. This is achieved in multiple ways. First, through seamlessly integrated data workflows that mirror each scientist’s lab workflow. Second, by the automation of data flows from instruments to digital experiment capture. And third, by cross-functional workflows that span members from diverse teams.
Solving Your Challenges

With Dotmatics You Can

icon Support seamless multidisciplinary workflows

Discovery workflows are complex, highly iterative and require many hand-offs between different scientific teams.
Dotmatics provides comprehensive solutions that maps on to all stages of a discovery workflow, irrespective of a project’s therapeutic modality. Capabilities to capture experiments, entities, samples and assay results are all built on a common platform. The platform allows seamless inter-connectivity, with a simple user experience. For example, from within an Electronic Laboratory Notebook (ELN) experiment, a medicinal chemist or molecular biologist can capture their procedures, and send the resulting entities to be registered and samples to inventory, without leaving the ELN interface. The same platform makes analysis workflows equally simple. It allows any scientist to collect all relevant project data about their entities and assay results, and then visualize and analyze that data without handing off between applications. When work crosses scientists or teams, a work requesting capability allows one team to request work from another, monitor progress and be informed when results are available.

Seamless workflow for antibody discovery

Seamless workflow for small molecule discovery

icon Capture your breadth of science

The Dotmatics solutions supports your research whatever the target modality. You can capture your experiments, and search for and analyze you project data, whether you are focused on small molecules, biologics, chemically-modified biologics, conjugates, cell therapies or any other modality. The applications are underpinned by scientific intelligence that understands molecular structures and/or the biological sequence of entities, in addition to text and numerical data. As scientific research continues to push the boundaries of what is possible, for example in new and different forms of chemically-modified biologics, the Dotmatics solution has been designed to quickly accommodate previously unknown therapeutic types to keep pace with the evolving science.

Learn more about Dotmatics solution for Chemically Modified Therapeutics Discovery

icon Capture your experiments, entities, samples and assays

The Dotmatics solution provides capabilities that capture entire laboratory workflows. A flexible Electronic Lab Notebook (ELN) provides templates to capture a wide range of experiments from medicinal chemistry to molecular biology to analytical sciences. Entity registration then captures the products of those experiments whether they are biologics, chemically-modified biologics, conjugates, small molecules or structure-less entities such as cell lines. The registration system tracks lineages of those entities as one is produced from its parent, and also relationships across entity types.  An inventory capability captures the locations and amounts of the physical samples and enables them to be sent for assay. The flexible assay data management system captures assays and their results. Supported assay types include high throughput, high content, dose-response, kinetic and DMPK experiments. All data is stored and connected in the platform so that once published, it is immediately available to the entire project team for analysis and decision making.

icon Automate lab data capture and processing

The Dotmatics lab data automation capability can greatly increase the efficiency of the lab. Data is automatically gathered from lab instruments and securely stored in a data lake. It is then parsed to extract data and meta-data, and validation can be performed. Operational dashboards allow progress and outcomes to be monitored. And finally the data can be sent directly to the lab notebook or assay data management systems. All this happens in real-time and without human intervention. This frees up scientists’ valuable time from mundane data gathering and processing tasks. It reduces or eliminates human-error, ensuring that data are clean and comprehensive when used to drive AI/ML models, or directly in scientists’ decision-making. The system is scalable to handle the huge numbers of files that can be generated by today’s highest throughput instruments.


Learn more about Dotmatics lab data automation solution

icon Support decision making with data intelligence

Using Dotmatics’ query capabilities, scientists can eliminate the effects of data silos by searching across aggregated data. Those data can be held in the Dotmatics system, in other in-house software and in external databases. The data are accessible in single, searchable project views. Structure- and sequence-searching capabilites allow all scientific data to be readily discoverable. Easy-to-use analytics included in Dotmatics’ data visualization capabilities allow project teams to analyze and visualize their data on a common platform. This allows for integrated decision-making and ultimately drives faster and best-informed decisions.

Learn more about Dotmatics data intelligence solutions

Learn more about Dotmatics solutions for chemistry design

icon Optimize collaborative networked research

Dotmatics’ software is designed for collaboration between scientific teams within an organization or, when cloud hosted, across a collaborative research network of pharmas, biotechs, CROs and academic labs. Scientific data can be shared in real time. Event feeds and dashboards show up-to-date project status. Collaboration and communication tools facilitate interaction between distributed teams requesting work and then sharing experiments and results.

Learn more about Dotmatics solutions for collaboration networks


Learn How Dotmatics Helped Optimize Discovery at LeadPharma

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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.

  • Provides scientific search, such as chemical substructure/similarity and sequence similarity/alignment
  • 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.

  • 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 Register

Dotmatics Register is a web-based compound and batch registration system used to maintain corporate chemical registration and reagent databases.

  • Captures chemical structure and associated data for newly synthesized or acquired compounds
  • Determines uniqueness and assigns new corporate IDs and/or new batch/lot IDs
  • Allows for single compound or batch registration
  • Allows registration from its own UI or from an ELN (Dotmatics or third party)

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 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 Blueprint

Blueprint is a web-based visualization and scientific analytics application. It is designed to help project scientists working on small molecule discovery projects to visualize and analyze their data, and to help them to design their next set of compounds to make.

  • Simple guided web user interface designed for bench scientists who are not data analysis experts and may not spend all day, every day in data analysis tools
  • Interactive visualization of scientific data with charts, tables and grids designed to explore molecular datasets
  • A carefully curated set of the more important workflows for chemistry calculations and cheminformatics analytics to understand SAR data sets
  • Enables communication through shared workspaces
  • Seamless integration to the Dotmatics suite:
    • Browser to assemble project data
    • Reaction Workflows to design libraries and chemical series
    • Vortex to enable deeper ad-hoc analysis

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 Chemselector

Dotmatics Chemselector manages very large chemistry datasets with fast search and trivially simple maintenance/update. It has a modern user interface focused on browsing and filtering for molecule, reagent and sample selection. The available eMolecules+ for Chemselector dataset provides access to highly curated eMolecules sourcing data.


  • High performance chemical searching, filtering and selection designed to support critical medicinal and synthetic chemistry workflows including:
    • building block selection
    • fragment set design
    • screening molecule selection for scaffold hopping
    • chemical series validation for hit to lead campaigns (“SAR by catalog”)
  • Uses Dotmatics provided datasets such as eMolecules+ for Chemselector and ChEMBL for Chemselector, or datasets built in-house from corporate or public databases

eMolecules+ for Chemselector

  • A sourcing dataset of over 20 million compounds and 8 million unique chemical substances with availability, pricing and packaging information from hundreds of suppliers using data curated by eMolecules
  • Provides additional information to the eMolecules source data to enhance searching, including deprotected structures, calculated physicochemical properties and structure classes
  • Simple monthly updates provide the latest eMolecules supplier and catalog 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 auto populate experiments to execute them
  • Teams can see request status and monitor compound or sample progression

iconDotmatics Reaction Workflows

Dotmatics Reaction Workflows is a graphical environment that enables scientists to build and execute data processing workflows to perform common cheminformatics tasks, such as library enumeration, structure normalization and compound profiling. Users build workflows in a drag-and-drop environment by selecting and connecting nodes that provide inputs (e.g a list of reagents) and outputs (e.g. view in Dotmatics Vortex) or perform actions (e.g. perform a reaction), configuring them with data and then executing the workflow to produce results. Many different tasks can be configured including:

  • Synthetic library enumeration for an ELN experiment
  • Virtual library enumeration and profiling for virtual screening
  • Structure normalization for registration
  • Idea generation via lead hopping or to avoid liabilities
  • Chemistry file clean up

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 Pinpoint

Dotmatics Pinpoint is a chemical cartridge for indexing and searching chemistry within Oracle databases.

Pinpoint enables indexing of chemical structures, calculations of physical chemical properties and substructure searches within an Oracle database. It is used to support structure searching with Dotmatics Browser, check for structural uniqueness and register molecules in Dotmatics Register, and store and search chemical reactions in Dotmatics Studies Notebook.

iconDotmatics Elemental

Dotmatics Elemental is a chemical sketcher that enable scientists to draw, edit and save structures and reactions, and calculate properties.

  • Sketch molecules, reactions and structure queries
  • Calculate chemical properties
  • Available as a fully-featured desktop application, iOS app or lightweight JavaScript plugin for sketching in-line in webpages

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