Future cheminformatics


Mobile apps, web interfaces, cloud computing, software as a service: collectively these make up the platform of the future. Chemistry software is making the transition, and Molecular Materials Informatics is at the forefront, with a catalogue of apps for sophisticated workflows, education and reference material. Backed up by best of breed cheminformatics algorithms running on cloud-hosted webservers, these tools can be used to accomplish complex tasks that were previously the exclusive domain of desktop computing.

Modern computing platforms provide numerous benefits over legacy desktop applications: low cost, ultimate ease of deployment, no system administration, and elegant user interfaces with low barriers to learning. Most scientific software in use today is based on software design principles that were appropriate for workstations of the 1980s. Three decades later, consumer internet software provides the reference point for what is now referred to as the user experience. At Molecular Materials Informatics, we believe we can provide that level of quality, and solve hard scientific problems at the same time.

Content creation


Creating new content on a mobile device is tricky for chemistry because so many tasks require a good way to draw chemical structure diagrams. Small touchscreens are not well suited for the legacy user interface design, so the concepts of drawing chemical diagrams have been redesigned to match the capabilities and limitations of the mobile touchscreen. The gesture-based sketcher can be seen in MolPrime, and can be used to quickly draw perfect publication quality diagrams on a screen as small as that of an iPhone.

With the diagram drawing problem solved, the Mobile Molecular DataSheet (MMDS) app can be used to create reaction schemes and manage datasheets, which are collections of structures, reactions, scalar data and text annotations. The SAR Table app can be used to decompose structures into scaffolds and substituents, and analyse the relationships between structure fragments and activity.

Chemical collaboration


Handling data on modern platforms involves a lot of sharing: with the previous generation of software, a document would be normally edited with one monolithic desktop application. Nowadays a document typically needs to be passed between mobile apps, webservices, computation clusters and desktop applications to complete a workflow. More often than not data needs to be shared between multiple collaborators, who may be using a heterogeneous mix of software and platforms, then eventually published. In this data rich age, publishing means not only creating perfect quality graphics for viewing, but also preserving the raw data in a fully interpretable form.

All of the mobile apps produced by Molecular Materials Informatics make extensive use of interprocess communication. Molecules, reactions and collections can be sent out as email attachments, or unpacked from incoming email or downloaded from the internet. Chemical data can be rendered using many different graphics formats, such as bitmapped images, vector graphics (SVG and EPS) and even Microsoft Word or Excel documents, in which embedded structures and reactions are drawn as vector graphics objects that look equally great on screen or as part of a printed manuscript.

Using the MolSync app, documents can be shared collaboratively via Dropbox. Data can be uploaded to molsync.com and made available to the world as data or rendered content (e.g. example content), or tweeted directly from within a mobile app. Publicly shared data can be referenced by a molecular glyph, which can be captured using the Living Molecules app, which acts like a QR code reader & creator for chemistry data. Public content can be recognised by the Open Drug Discovery Teams (ODDT) app, which is a magazine-like reader for drug related content, which also happens to be chemically aware.

Online databases


One of the compelling use cases for mobile apps is providing a specialised client to lookup online databases. Pairing the structure-drawing technology from Molecular Materials Informatics with chemical databases is a perfect match: it is possible to search repositories such as ChemSpider, PubChem, ChEBI, eMolecules, SPRESI and Mobile Reagents using advanced structure searching techniques. Searching of online databases is built into the workflow capabilities of MMDS, SAR Table and MolPrime+, while specialised apps have been created for searching ChemSpider, SPRESImobile and Mobile Reagents.

Education


While some of the mobile apps created by Molecular Materials Informatics are designed with education in mind, all of them are relevant to chemists at any point in their career, from high school onward. Working with chemical data is a task that is relevant to experts and beginners alike: all chemists need to know how to draw structures correctly, lookup content online, access property calculations, and present the results. Consumer versions of the tools produced by Molecular Materials Informatics are either free or affordable to almost any demographic.

The MolPrime+ app has a number of calculation features based on individual structures, such as valence checking, molecular weight/formula calculation, mass spectroscopy distributions, calculation of physical properties, enumeration of tautomers, and stereochemistry (R/S, E/Z). Some of these calculations are carried out within the app, while others harness webservices to perform the underlying calculations. The Reaction101 app was created as a collaboration with Eidogen-Sertanty, and allows drawing of reactions, and provides tools to help balance them. Yield101 goes on to add basic laboratory functionality, by interconverting quantities such as grams and moles using all available information, thereby removing tedious calculation steps.

Data reference


Appification of data is a useful way to turn a mobile device into an on-demand interactive reference card. Several apps have been created to demonstrate this. The Approved Drugs app provides a compiled list (>1000) of FDA approved drugs, which can be browsed, viewed, searched or sorted by structural similarity. The app is a useful reference for drug repurposing. The TB Mobile app, produced on behalf of Collaborative Drug Discovery, provides access to otherwise hard to find structure-activity information about Tuberculosis inhibitors. The Green Solvents and Lab Solvents apps provide a list of commonly used organic solvents, with data about their environmental properties, which can be used to assist synthesis planning.

Core technology


The original technology developed by Molecular Materials Informatics consists of two parts: a core library for mobile apps, called MMDSLib, which is the basis for chemistry apps created for native iOS, Android and BlackBerry products. The core library provides functionality such as the gesture-based chemical diagram sketcher, and some moderately sophisticated cheminformatics capabilities that run on the mobile device.

Serverside technology is based on Java-based projects: com.mmi for core cheminformatics functionality, and com.molsync for the J2EE components that expose functionality to the web. The serverside functionality includes the following:

  • property calculation
  • tautomer enumeration
  • stereochemistry assignment (CIP rules)
  • model building for structure-activity relationships
  • manuscript quality structure rendering
  • cheminformatics format interconversion
  • graphics file creation, including clean room implementation of DocX and XlsX formats (Microsoft Office, with embedded vector drawings)
  • substructure searching
  • scaffold analysis and R-group decomposition
  • molecule and datasheet storage for public sharing
  • web interface for viewing chemical content and interconverting formats
  • meta-layer for searching chemical databases (ChemSpider, PubChem, ChEBI)
  • document collection system (Twitter, RSS) for the Open Drug Discovery Teams project

All of this support functionality is hosted on the server http://molsync.com, which is publicly accessible and is used by a variety of apps and other tools. For non-public use, the software can be licensed for internal deployment.

Contact: info@molmatinf.com

Recent News


19-Aug-2014
Green Lab Notebook
New app released: GLN, on the iTunes AppStore, for managing chemical reactions.
18-Aug-2014
PeerJ Paper
Recently published in PeerJ: Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation.
9-Aug-2014
TB Mobile v2 paper
Recently published in the Journal of Cheminformatics: New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.
24-Jul-2014
Valence
New app released: Valence, on the iTunes AppStore, for teaching introductory chemical bonding theory.
12-Apr-2014
Abstract in J.Cheminf.
Abstract for 2013 presentation at the German Chemical Society meeting in Journal of Cheminformatics. See also the actual slides.
19-Mar-2014
ACS Talks
From the Dallas meeting (March 2014): Green Lab Notebook and Cloud Computing .
13-Mar-2014
App Updates
MolPrime+ and SAR Table have both been overhauled for iOS 7.
20-Feb-2014
TB Mobile v2.0
The TB Mobile for iOS app has undergone a major upgrade and overhaul.
19-Feb-2014
MMDS v1.5.2
The searching capabilities of MMDS have been improved.
24-Jan-2014
MMDS v1.5.0
MMDS has been upgraded to iOS 7, as well as two major new features: simple pipelining and OpenPHACTS assays.
23-Dec-2013
MMDS v1.4.9
The Mobile Molecular DataSheet app now has an icon-based main menu and a much improved data importing sequence.
27-Nov-2013
iOS 7
Approved Drugs, Living Molecules and Open Drug Discovery Teams overhauled for iOS .
23-Nov-2013
MMDS v1.4.8
MMDS has a number of new sketching improvements.
15-Nov-2013
GDCh 2013
Slides for the German Chemoinformatics Conference available.
22-Oct-2013
NETTAB 2013
Slides for the Cheminformatics workflows using the mobile + cloud platform available.

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