Molecular Materials Informatics Inc.

Montreal, Canada

Molecular Materials Informatics Inc.

Montreal, Canada
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Ekins S.,Collaborations in Chemistry | Waller C.L.,Pfizer | Waller C.L.,University of North Carolina at Chapel Hill | Bradley M.P.,CollaborationFinder | And 2 more authors.
Drug Discovery Today | Year: 2013

Drug discovery is shifting focus from industry to outside partners and, in the process, creating new bottlenecks. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the USA, with little coordination or consideration of the outputs and creating a translational gap. Although there have been collaborative public-private partnerships in Europe to share pharmaceutical data, the USA has seemingly lagged behind and this may hold it back. Sharing precompetitive data and models may accelerate discovery across the board, while finding the best collaborators, mining social media and mobile approaches to open drug discovery should be evaluated in our efforts to remove drug discovery bottlenecks. We describe four strategies to rectify the current unsustainable situation. © 2012 Elsevier Ltd.


Williams A.J.,Royal Society of Chemistry | Ekins S.,Collaborations in Chemistry | Clark A.M.,Molecular Materials Informatics Inc. | Jack J.J.,Symyx | Apodaca R.L.,Metamolecular LLC
Drug Discovery Today | Year: 2011

Mobile hardware and software technology continues to evolve very rapidly and presents drug discovery scientists with new platforms for accessing data and performing data analysis. Smartphones and tablet computers can now be used to perform many of the operations previously addressed by laptops or desktop computers. Although the smaller screen sizes and requirements for touch-screen manipulation can present user-interface design challenges, especially with chemistry-related applications, these limitations are driving innovative solutions. In this early review of the topic, we collectively present our diverse experiences as software developer, chemistry database expert and naïve user, in terms of what mobile platforms could provide to the drug discovery chemist in the way of applications in the future as this disruptive technology takes off. © 2011 Elsevier Ltd.


Clark A.M.,Molecular Materials Informatics Inc. | Ekins S.,Collaborations in Chemistry | Williams A.J.,Royal Society of Chemistry
Molecular Informatics | Year: 2012

The proliferation of mobile devices such as smartphones and tablet computers has recently been extended to include a growing ecosystem of increasingly sophisticated chemistry software packages, commonly known as apps. The capabilities that these apps can offer to the practicing chemist are approaching those of conventional desktop-based software, but apps tend to be focused on a relatively small range of tasks. To overcome this, chemistry apps must be able to seamlessly transfer data to other apps, and through the network to other devices, as well as to other platforms, such as desktops and servers, using documented file formats and protocols whenever possible. This article describes the development and state of the art with regard to chemistry-aware apps that make use of facile data interchange, and some of the scenarios in which these apps can be inserted into a chemical information workflow to increase productivity. A selection of contemporary apps is used to demonstrate their relevance to pharmaceutical research. Mobile apps represent a novel approach for delivery of cheminformatics tools to chemists and other scientists, and indications suggest that mobile devices represent a disruptive technology for drug discovery, as they have been to many other industries. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Ekins S.,Collaborations in Chemistry | Clark A.M.,Molecular Materials Informatics Inc. | Williams A.J.,Royal Society of Chemistry
Molecular Informatics | Year: 2012

The Open Drug Discovery Teams (ODDT) project provides a mobile app primarily intended as a research topic aggregator of predominantly open science data collected from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload, delivering access to information that is highly relevant and focused on their topic areas of interest. Research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. These include rare and neglected diseases, and precompetitive and public-good initiatives such as green chemistry. The ODDT project uses a free mobile app as user entry point. The app has a magazine-like interface, and server-side infrastructure for hosting chemistry-related data as well as value added services. The project is open to participation from anyone and provides the ability for users to make annotations and assertions, thereby contributing to the collective value of the data to the engaged community. Much of the content is derived from public sources, but the platform is also amenable to commercial data input. The technology could also be readily used in-house by organizations as a research aggregator that could integrate internal and external science and discussion. The infrastructure for the app is currently based upon the Twitter API as a useful proof of concept for a real time source of publicly generated content. This could be extended further by accessing other APIs providing news and data feeds of relevance to a particular area of interest. As the project evolves, social networking features will be developed for organizing participants into teams, with various forms of communication and content management possible. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Ekins S.,Collaborations in Chemistry | Clark A.M.,Molecular Materials Informatics Inc. | Williams A.J.,Royal Society of Chemistry
ACS Sustainable Chemistry and Engineering | Year: 2013

Green Chemistry related information is generally proprietary, and papers on the topic are commonly behind pay walls that limit their accessibility. Several new mobile applications (apps) have been recently released for the Apple iOS platform, which incorporate green chemistry concepts. Because of the large number of people who now own a mobile device across all demographics, this population represents a highly novel way to communicate green chemistry, which has not previously been appreciated. We have made the American Chemical Society Green Chemistry Institute (ACS GCI) Pharmaceutical Roundtable Solvent Selection Guide more accessible and have increased its visibility by creating a free mobile app for the Apple iOS platform called Green Solvents. We have also used this content for molecular similarity calculations using additional solvents to predict potential environmental and health categories, which could help in solvent selection. This approach predicted the correct waste or health class for over 60% of solvents when the Tanimoto similarity was >0.5. Additional mobile apps that incorporate green chemistry content or concepts are also described including Open Drug Discovery Teams and Yield101. Making green chemistry information freely available or at very low cost via such apps is a paradigm shift that could be exploited by content providers and scientists to expose their green chemistry ideas to a larger audience. © 2012 American Chemical Society.


Clark A.M.,Molecular Materials Informatics Inc. | Sarker M.,SRI International | Ekins S.,Collaborative Drug Discovery, Inc.
Journal of Cheminformatics | Year: 2014

We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. Results: We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP-6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. Conclusions: TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool. © 2014 Clark et al.


Ekins S.,Collaborative Drug Discovery, Inc. | Clark A.M.,Molecular Materials Informatics Inc. | Sarker M.,SRI International
Journal of Cheminformatics | Year: 2013

Background: An increasing number of researchers are focused on strategies for developing inhibitors of Mycobacterium tuberculosis (Mtb) as tuberculosis (TB) drugs. Results: In order to learn from prior work we have collated information on molecules screened versus Mtb and their targets which has been made available in the Collaborative Drug Discovery (CDD) database. This dataset contains published data on target, essentiality, links to PubMed, TBDB, TBCyc (which provides a pathway-based visualization of the entire cellular biochemical network) and human homolog information. The development of mobile cheminformatics apps could lower the barrier to drug discovery and promote collaboration. Therefore we have used this set of over 700 molecules screened versus Mtb and their targets to create a free mobile app (TB Mobile) that displays molecule structures and links to the bioinformatics data. By input of a molecular structures and performing a similarity search within the app we can infer potential targets or search by targets to retrieve compounds known to be active. Conclusions: TB Mobile may assist researchers as part of their workflow in identifying potential targets for hits generated from phenotypic screening and in prioritizing them for further follow-up. The app is designed to lower the barriers to accessing this information, so that all researchers with an interest in combatting this deadly disease can use it freely to the benefit of their own efforts. © 2013 Ekins et al.; licensee Chemistry Central Ltd.


Clark A.M.,Molecular Materials Informatics Inc.
Molecular Informatics | Year: 2013

The creation of 2D molecular structure diagrams that make full use of the capabilities of modern display systems, using only input data expressed in file formats used for cheminformatics, is a complex task that requires a number of additional algorithms. Assuming that atom positions have been well chosen, the rendering engine is required to micromanage the precise positioning of atom labels, bonds and atom adjuncts, in such a way that the final output is correct, consistent with convention, and as pleasing to the eye as a diagram produced by a graphic designer. The techniques must be equally applicable when creating output for low-resolution screens and high resolution printed output, and make use of contemporary graphics file formats in such a way that the largest possible number of software platforms are able to display the output at any resolution without degradation or inconsistency. The main issues involved in meeting these criteria are discussed, and algorithms for satisfying them are presented. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Clark A.M.,Molecular Materials Informatics Inc.
Journal of Chemical Information and Modeling | Year: 2011

Most data structures used to represent molecular entities for cheminformatics are underspecified for purposes of representing nonorganic chemical species. Two extensions are proposed: allowing bond orders of 0 and adding an atom property to control the number of inferred attached hydrogen atoms. The case for these two extensions is made by demonstrating the effective representation of a number of unconventional bonding types that cannot be effectively represented by data structures currently in common use. A set of enhancements to the industry standard MDL CTfile format is proposed, which includes a backward compatibility mechanism to maximize interpretability by software that has not been updated to make use of the extensions. © 2011 American Chemical Society.


Clark A.M.,Molecular Materials Informatics Inc.
Journal of Cheminformatics | Year: 2010

A collection of primitive operations for molecular diagram sketching has been developed. These primitives compose a concise set of operations which can be used to construct publication-quality 2 D coordinates for molecular structures using a bare minimum of input bandwidth. The input requirements for each primitive consist of a small number of discrete choices, which means that these primitives can be used to form the basis of a user interface which does not require an accurate pointing device. This is particularly relevant to software designed for contemporary mobile platforms. The reduction of input bandwidth is accomplished by using algorithmic methods for anticipating probable geometries during the sketching process, and by intelligent use of template grafting. The algorithms and their uses are described in detail. © 2010 Clark; licensee BioMed Central Ltd.

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