Dotmatics Solution for Chemistry Design Solution

Self-Service Data Analysis and Design for Chemists

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Facilitating Data-Driven Decision Making in Small Molecule Discovery

The small molecule discovery process is becoming ever more data-driven. The analysis of scientific project data to drive decisions on the progression of chemical series is a critical activity in each discovery cycle. The Dotmatics solution for chemistry design empowers medicinal and synthetic chemists with analysis tools designed from the ground-up for them. This helps them make the best-informed decisions. It can also relieve the burden on data-scientists and computational chemists, ensuring that each cycle in the discovery process can be completed as efficiently as possible.

Your Challenges

Do you need

Chemist Icon

Software designed for chemists

Too often visualization and analysis tools are designed for data scientists or computational chemists. They are powerful, but require dedicated expertise that can be limited in its availability. So projects decision can be fully informed but must wait for that resource, or can be timely but may have to be based on less than complete data and analysis. A solution designed for use by chemists themselves can support decision making that is both best-informed and timely

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Seamless workflows

From one round of synthesis to the next there are many important tasks: collecting and organizing all of the project’s SAR data, visualizing and analyzing it, applying models to making decisions and then designing the next molecules or library.  Chemists should be guided through these in a continuous workflow, without needing to use multiple disjointed applications or having to ever move data manually between programs

Decision Support Icon

Real-time data driving decisions

Project meetings and reports are often based around static snapshots of project data. These rapidly become stale, and are typically assembled manually so prone to error. All members of the project team should have real-time access to all the project data throughout the data review and decision making processes.


With Dotmatics you can

icon Assemble all relevant project data

One of the hardest challenges in data analysis can be assembling a complete set of project data in the first place. The Dotmatics search capability allows project scientists to search and gather all relevant project data, irrespective of whether it is in Dotmatics databases, scattered across multiple third party systems or in corporate datamarts or warehouses.

Using the search capability allows all relevant project data to be assembled for analysis, without the need to manually join data that has been collected in multiple applications, ensuring that errors are not introduced before analysis. Exploratory queries can be run on demand, or standard project queries defined and run on an automated schedule to identify the latest data.

icon Visualize and analyze project data in a simple guided web application.

They key to our solution is a visualization and cheminformatics application that provides a simple guided web user interface. This is explicitly designed for bench scientists who are not data analysis experts and may not spend all day, every day in data analysis tools. It provides

  • 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 cheminformatics analytics ranging from property calculations and program metrics, to R-group analysis and match-molecular pairs analysis. Each workflow is guided by a wizard to walk the user step-by step through the analysis and results
  • The application allows workspaces, datasets and analysis to be shared. This enables team-based decision making ensuring that every member is working from exactly the same data and analysis.

Learn more about Dotmatics Blueprint

icon Design new molecules/series/libraries or select available compounds/libraries for purchase

An interactive design environment allows chemists to build and execute workflows to

  • Design and enumerate synthetic libraries and automatically create experiments in the Notebook for execution
  • Enumerate virtual libraries for profiling, selection or virtual screening
  • Use chemical transformations to suggest novel molecules for lead hopping or to avoid liabilities

With Dotmatics high speed chemistry search, massive databases of available reagents (such as the e-Molecules collection) can be used to quickly identify available reagents sets for library enumeration. The same capability can be used to filter commercially available screening compound collections to identify those to purchase to augment corporate collections, or to expand known SAR for a project

icon Create end-to-end workflows

The entire process of gathering all project data, and then loading it into the analysis application is fully integrated and straightforward. This removes any point at which files need to be moved manually preventing cut-and-paste errors that might occur. The roundtrip from analysis back to dataset browsing is also part of the fully integrated workflow, so for example an interesting subset of molecules can be selected during analysis and then returned as a new hitlist, which in turn can then be used to set up a work request for those compounds to be screened in a follow up assay panel.

Once enumerated, design libraries can be loaded directly into analysis to select a subset for synthesis and then these can be used to automatically experiments in the ELN ready for their synthesis. Once again, there is no manual data manipulation, so the process is error-proof and maximally efficient.

icon Access real-time data for decision making

Regular project team meetings to review project data and make decisions about future directions are a standard part of the drug discovery process. Very often these review data snapshots that are manually assembled into PowerPoint presentations. The manual assembly of these is time consuming and prone to error. The data once assembled, is static, as are the views that are reviewed during the meeting.

Reviewing data that is stale, and may have errors, can lead to decisions that may not be the best, and may take the project down the wrong path. Reviewing static views does not allow for “what-if” brainstorming discussions during team meetings

Using the Dotmatics visualization solution as a portal into live data during project meetings ensures that the data is accurate and up-to-date, and allow views to be refined on the fly to allow real-time data exploration while brainstorming.


Empower Your Bench Scientists

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This solution consists of

iconDotmatics Browser

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 project 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: 

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 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 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 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