Dotmatics Solutions for Small Molecule Discovery

End-to-end Workflows to Support Discovery Project Teams

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Enhancing efficiency and supporting innovation

Dotmatics’ solutions support small molecule discovery from hit and lead identification, through lead optimization, to candidate selection. Fully integrated laboratory informatics capabilities capture instrument data, experiments, molecules, samples and assays. Decision support tools enable gathering, analysis and visualization of project data. Together, these help project teams be more efficient and make better informed decisions faster.

Your challenges

Do you need

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To collaborate?

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

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Decision support?

Every member of the project team needs real-time access to all the project data for which they have permission, irrespective of where it is stored. This ensures that they can make the best-informed decisions about project progression.

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Increased lab efficiency?

Increasing efficiency will reduce discovery cycle times. This can be achieved with seamless integrated data workflows that mirror each scientist’s lab workflow, by the automation of data flows from instruments and by cross-functional workflows that span diverse team members.


With Dotmatics You Benefit From

icon Seamless Multidisciplinary Workflows

Dotmatics’ capabilities are fully integrated so that scientists can easily follow their workflows through the software.

Work-requesting capabilities enable cross-team workflows to be created and monitored.

icon Laboratory Informatics for Medicinal Chemists

Integrated workflows allow chemists to capture medicinal chemistry experiments and analytical results. They can register the resulting entities and track associated samples, and then request analytical and assay services on their compounds.

icon Laboratory Informatics for Assay Scientists

Integrated workflows allow assay scientists to initiate screening experiments from in-bound requests. They can capture and analyze data from primary, secondary and DMPK assays in Studies. Once complete they publish validated assay results directly to the scientific teams.

icon Decision Support for the Entire Team

All team members can search across all research data including experiments, molecules, samples and assays as soon as results become available. Cheminformatics analysis and high-performance visualization of project data enable the team to make well-informed decisions about project progressions. Compound designers can use molecule and library design tools to propose new molecules. Real-time dashboards support project management decision making.

icon Collaborative Workflows

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, and collaboration and communication tools facilitate interaction between distributed teams.

Find out more about how you can use Dotmatics to improve your collaboration:

Collaboration Solution

icon Instrument Data Automation

Dotmatics lab data automation platform can greatly increase the efficiency of the lab. Data can be gathered from instruments and securely stored in a data lake. It is then parsed to extract data and meta-data and validation can be performed. The data can then be sent directly to the lab notebook or assay data management systems. All this can happen in real-time and without human intervention. This frees up valuable scientists time from mundane data gathering and processing tasks. It eliminates human-error, ensuring that data is clean and comprehensive when used to drive AI/ML models, or directly in scientists’ decision making.


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Learn How Dotmatics Has Helped Improve Debiopharm's Workflow

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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 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 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 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 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


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 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 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 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

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)

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