Desktop

OS X Molecular DataSheet

Mobile

Mobile Molecular DataSheet

Features

Structure drawing

Data management

Mobile collaboration

Chemical lookup

Document preparation

Property calculation

Green Lab Notebook

SAR Table

PolyPharma

MolPrime

Approved Drugs

Valence

Green Solvents

Lab Solvents

ChemSpider Mobile

SPRESImobile

TB Mobile

Web

WebMolKit

SketchEl

MolPress

Services

Toolkits

Collaboration

Medicinal Chemistry Toolkit

Desktop


OS X Molecular DataSheet


The OS X Molecular DataSheet (XMDS) app is a Mac app that combines a speadsheet-like editor for chemical data with an advanced structure editor. The app is designed for content creation first and foremost, with an extremely effective sketcher and additional tools for drawing chemical reactions. It has been uniquely designed as a native Mac OS X app, to provide the best possible user experience.


Mobile



Mobile Molecular DataSheet


The Mobile Molecular DataSheet (MMDS) is the original, pioneering cheminformatics app for mobile devices, which was first released in 2010. It implements core chemical structure technology and delivers it in the form of a powerful app that runs on all phone and tablet form factors. MMDS provides the ability to draw presentation quality 2D structure diagrams, with productivity comparable to desktop-based sketchers. The user experience operates on the datasheet, which is a molecular spreadsheet that holds chemical structures, reactions, text, numbers, etc. The app can be used as a hub for interoperability, and can exchange data with other chemically aware apps, as well as being used to access webservices and create graphics suitable for use in manuscripts.

The MMDS app is the most powerful app from Molecular Materials Informatics. It is available for all iOS devices via the iTunes App Store. Unlike any other drawing technology, the structure drawing interface is effective on touchscreen devices of any size, allowing large and complicated molecules to be drawn on a palm-sized iPhone just as effectively as with a tablet, a laptop, or a desktop computer. The features that were originally designed for MMDS have been incorporated into a number of other apps, which provide more specialised capabilities.

Features


Structure drawing


Chemical structure drawing is a key feature of MMDS, and is the fundamental component that allows the app to be used for content creation as well as consumption. The editor is finely tuned to each device environment, and has a sophisticated set of tools to make drawing chemical structures fast and efficient, within the constraints of the user interface capabilities. A chemical reaction editor is also available, which is based on the structure editor for individual reaction components.

Data management


Molecular structures and reactions are assembled into chemical datasheets, which are used to group structure diagrams with text and numeric information. These datasheets can be composed, edited and browsed, all on an ultraportable device. Prior to MMDS, this could only be done on a laptop-or-bigger device. Managing chemical data is now much more viable for mobile contexts such as commuting by train, plane or bus. All of this functionality is provided as a native app, and so does not require internet connectivity, which is important for air travel or underground journeys.

Mobile collaboration


Data can be exchanged in a variety of ways, the most convenient being by use of email attachments. Colleagues can use MMDS to keep in touch by passing chemical data to each other whenever the device has access to the internet. Attachments use standard formats, and can interoperate with any other email client. Opening a chemical data attachment from any source allows it to be conveniently imported into MMDS, and viewed or edited right away. Chemical documents can also be opened from the web browser, and data also can be moved around using standard filesystem access.

Chemical lookup


By using the built in webservice client to access online chemical databases, MMDS can be used for structure searching, which is a feature that is otherwise generally unavailable for mobile devices. The webservice uses a federated middleware platform, which combines results from ChemSpider, PubChem and ChEBI.

Document preparation


MMDS has a strong focus on aesthetics, and it is capable of producing high quality pictures of structures and reactions. It can be used to transport chemical data to other apps running on the device, using the clipboard. It is also possible to copy high resolution images, which can be used by presentation software, such as Pages or Keynote for iPad. This capability means that it is now possible to create a document or presentation with chemical diagrams using only a mobile device.

Property calculation


Numerous structure-based properties can be calculated from within the app, from trivial derivatives like molecular formula, to more difficult calculations like log P, to molecular properties like stereochemistry, tautomers, mass distribution, valence violations, PAINS filters and Bayesian models.

Green Lab Notebook


The Green Lab Notebook is a structure-centric tool for capturing chemical reactions. Multistep reactions are drawn out by individual components, which can be balanced and associated with corresponding properties. Green chemistry metrics are calculated automatically.

Features:

  • Draw reactions with precise detail: component roles, structures and stoichiometry all captured reliably.
  • Multistep reactions represented in an informatically rich way, preserving stoichiometry.
  • Built in access to green solvents.
  • Automatic, always-on calculation of green chemistry metrics such as atom economy, process mass intensity and E-factor.
  • Strong import, export, sharing and graphics creation capabilities.
  • Advanced sketcher for publication quality drawings, and capable of handling hard-to-represent organometallic and inorganic reagents.
  • For an introductory article, see: Green Lab Notebook.

The Green Lab Notebook is

SAR Table


SAR Table provides a convenient way to produce tables of structures and activity or property data, by providing scaffolds, substituents, and data.

Features:

  • Draw scaffold and substituents: the whole molecule is constructed automatically.
  • Numerous features for duplicating data content, to minimise the amount of re-drawing of structures.
  • Associated data can be entered: identifiers, text and property data (with units and modifiers).
  • Designed for creating new tables of structure-activity data for publication/collaboration, and for re-entering data from existing publications, with minimum effort.
  • Automatically assign scaffolds-to-molecules and derive implied substituents using a substructure matching service.
  • Content is stored in a datastructure which stores the scaffold/substituent breakdown, the whole molecule, and the data, all together, so it can be used for creating documents, and for applying cheminformatics techniques.
  • Data can be passed around by email, and used to generate or print PDF files.
  • Tables can be converted to graphics formats, including HTML with embedded SVG graphics, and Microsoft Word and Excel documents, with structures rendered using DrawingML vector graphics.
  • For an introductory article, see: Introduction to SAR Table (iOS).

SAR Table is

PolyPharma


The PolyPharma provides powerful model prediction and visualisation capabilities for computer aided drug design.

Features:

  • Hundreds of Bayesian models loaded onto the app, for disease targets and off-targets.
  • All predictions and visualisations performed on the device: no internet access required.
  • Lookup or add custom structures: access predictions for all models.
  • Colour-coded heatmaps, and structure overlays for correlating structure regions with activity or lack thereof.
  • Honeycomb clustering for interactively exploring the structure-activity neighbourhood, in context of the molecules used to build the target molecules.
  • For an introductory article, see: PolyPharma.

PolyPharma is

MolPrime


MolPrime+ is a simplified app that concentrates on allowing molecular structures to be drawn and utilised on a mobile device (iPhone, iPod, iPad and Android devices). The app uses the same powerful sketcher as the Mobile Molecular DataSheet.

Features:

  • Draw new structures from scratch, using the powerful MMDS structure editor.
  • Use recently drawn structures as a starting point.
  • Review calculated properties, and check to see if the structure has any obvious mistakes, such as pentavalent carbons.
  • Access additional calculated properties, such as log P and molar refractivity, via remote procedure call (MolPrime+ only).
  • Use structures to search databases such as Mobile Reagents or ChemSpider, or search ChEBI and PubChem directly within the app (MolPrime+ only).
  • Send structure data and images via email.
  • Copy structure images onto the clipboard for pasting into other apps.
  • Generate Microsoft Word documents (.docx) with structures rendered using embedded vector graphics (MolPrime+ only).
For a high level overview, see Slideshare Presentation.

MolPrime+ is

Approved Drugs


The Approved Drugs app presents over a thousand drug structures and names from the list approved by the Food & Drug Administration (FDA).

Features:

  • The structure diagrams are shown on the main screen, and can be browsed, searched by name, filtered by structural features, or sorted by similarity to a reference structure.
  • Individual drugs can be viewed in 2D or 3D, along with tautomers, and links to other apps and reference material.
  • It is also possible to use Bayesian models to predict relevant probabilities, such as water solubility, Lipinski probelikeness, KCNQ1 and hERG avoidance, and activities vs. several diseases.
  • For an introductory article, see: Approved Drugs.

Approved Drugs is

Valence


The Valence app is an educational tool for teaching Lewis octet bonding theory to students, at the late high school/ early undergraduate level.

Features:

  • Drag electrons into bonds or lone pairs to complete molecular structure.
  • Interactively view 3D models of results, to understand geometry.
  • 5 categories of instruction:
    1. Main group hydrides
    2. Multiple bonds
    3. Small molecules
    4. Polyatomic anions
    5. Octet exceptions
  • Incredibly simple interface: no practice needed.
  • Review questions and background material.
  • Use with curriculum or for independent learning.

For a more detailed description, see Valence App.

Valence is

Green Solvents


Green Solvents is a reference-card app that provides relevant information on the safety and environmental properties of commonly used lab solvents. Structures, names and environmental hazard ratings are available, as well as quick links to online resources for more detailed information.

Green Solvents is

Lab Solvents


Lab Solvents is a reference app that provides information on a number of common laboratory solvents. The list of solvents can be browsed, selected by category, filtered by health, safety and environmental properties, or sorted by similarity to a provided reference structure.

Each solvent can be examined for more information, such as physical properties, formula/weight, links to ChemSpider, and greenness ratings from the ACS Green Chemistry Institute and GSK Solvent Selection Guide.

Lab Solvents is an

ChemSpider Mobile


ChemSpider Mobile was built by Molecular Materials Informatics on behalf of the Royal Society of Chemistry, in order to provide iOS and Android users with mobile access to the popular ChemSpider online database. Both versions of the app provide text and structure searching capabilities. Results an be browsed by structure and name, and opened within the mobile browser for more details.

For a detailed description of the product, see: ChemSpider Mobile

SPRESImobile


SPRESImobile is a free app for searching the SPRESI ChemReact data collection. Molecules can be searched by name and structure. The results can be browsed, including their corresponding reactions, and literature references. The SPRESImobile app is the result of a collaboration between InfoChem GmbH, Eidogen-Sertanty and Molecular Materials Informatics.

SPRESImobile is

TB Mobile


The TB Mobile app provides information on ~800 compounds that have been evaluated for biological activity against the tuberculosis mycobacterium, which includes more than 90 specific targets. The app allows structures and targets to be browsed on the main screen, as well as searched by text, sorted by structure, and filtered by a variety of criteria. Details on individual targets and their biological activity can be examined.

The app is available for both iOS and Android devices. Version 2 of the app (iOS only) adds improved similarity techniques, interactive 2D clustering, personal collections and target prediction.

The app was developed as a collaboration between Collaborative Drug Discovery and Molecular Materials Informatics, designed by Sean Ekins, and funded by the National Institute of Allergy And Infectious Diseases.

Web


WebMolKit


WebMolKit is an open source web library that is hosted on GitHub. The source code is all TypeScript, which is cross-compiled to JavaScript so it can be run on any modern browser. The library provides core cheminformatics functionality (e.g. representing and drawing molecules) and an interactive sketcher. It is available to anyone under the Gnu Public License v3, or other licenses by special arrangement.

SketchEl


The SketchEl2 project is a wrapper around the WebMolKit library, using the Electron framework to deliver the sketcher functionality on the desktop. This essentially means that it uses a stripped down version of the Chrome browser to make a web-native app into a first class citizen on Windows, Linux or Mac.

MolPress


The MolPress plugin is a collection of features for use with WordPress to represent molecular objects (molecules, reactions, datasheets) within otherwise ordinary blogging pages. Transforming a  WordPress site in this way allows chemistry to be displayed visually while also storing the machine readable data. The project is open source, and hosted on GitHub.

Services


Molecular Materials Informatics is engaged in a number of service contracts, some of which are public knowledge. For more information, see contact page.

Toolkits


The Apple-centric products for macOS and iOS are based on a common core, written in Swift (for newer products) or Objective-C. These toolkits have been used for a number of collaborative products, in particular mobile apps create by third parties who need sophisticated chemistry software functionality to be integrated within their products.

In addition to front-facing products for desktop, mobile and web, highly advanced cheminformatics functionality is encapsulated in a Java-based library. These tools are used to host back-end service websites (e.g. molsync.com), for data preparation purposes, and for several ongoing collaboration efforts.

Collaboration


Molecular Materials Informatics has a number of ongoing collaborations, some of which involve building apps on behalf of other companies and organisations, and others for which key technology components are licensed for third party apps.

Medicinal Chemistry Toolkit


The Medicinal Chemistry Toolkit is a companion app for the The Handbook of Medicinal Chemistry: Principles and Practice textbook from the Royal Society of Chemistry. It includes chemical structure drawing functionality from Molecular Materials Informatics, as well as the ability to calculate structure-based properties such as log P, and to determine when any of the Astra-Zeneca filters apply to the structure. The latter functionality was developed specifically for this app in order to educate upcoming chemists about what kinds of chemical fragments are suitable for drug-like molecules.

The app is free on the iTunes AppStore and runs on iPad devices.