EUGM 2013 - Andras Stracz (ChemAxon) - ChemAxon Plexus: A desktop application using web technology

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We introduce ChemAxon Plexus, a new web application that integrates ChemAxon’s discovery tools into a clean and user friendly desktop tool for chemists. Launch features focus on compound library design and the tools supporting this; database management, chemical searching, library enumeration, phys-chem property calculation, virtual synthesis and similarity searching. We describe the integration of existing products, and a fresh take on their user interfaces to make them easier to use while keeping the essence and utility intact. We demo Plexus and its simplified Markush structure editor, a user interface for virtual screening and how effortless reaction setup can be.

Technology

chemicalize.org
Content discovery
Utility
UI prototyping

chemicalize.org - Content
Chem Search database
Webpage Viewer usage
18k
users
423.000
webpages
642.000
names
378.000
structures

chemicalize.org - Content quality
in PubChem: 90k novel structures
http://chemicalize.org/url/pubchem
378.000
structures
40+ citations since 2012
http://goo.gl/FQS1L

chemicalize.org - Utility
article in JChemInf by Christopher Southan and
Andras Stracz, DOI:10.1186/1758-2946-5-20
... demonstrates the utility of chemicalize.org for
the exploration of chemical structure connectivity
between documents and databases ...
... flexibility to extract text from any internal,
external or Web source. It synergizes with other
open tools ...

chemicalize.org - UI
review in JCIM by Matt Swain, Univ. Cambridge
DOI: 10.1021/ci300046g:
... the intuitive interface lends itself well to learning by trying
...
... the simplicity of this interface ... is quite refreshing ...
it is common to be bombarded by long forms with
dozens of options ...

chemicalize.org - mobile
● mobile traffic is growing
● keep experimenting
● apps:
○ native feel
○ performance
○ unlock new features
● building on the existing mobile site

chemicalize.org - mobile apps
● grab the app in the Play Store
● coming soon to iTunes

Plexus
Versatile
● Thin client, web service base
● Deployable in all scenarios
○ PC/Mac
○ internal network
○ external partners
○ cloud

Plexus
Versatile
User friendly
● design: consistent web app look & feel
● high visibility of important actions
● layout: clear and structured, fluid
● UX: fast, streamlined, intuitive solutions
● Marvin for JavaScript fits perfectly

Plexus
Versatile
Workflow oriented
discovery tool
User friendly
● Focus: Library design
● Modular

Data table
● table view for your data, expected features
● import:
○ any chemical structure file format
○ office documents
● export:
○ any chemical structure file format
○ JChem for Excel workbook
● fast, looks great
● easily add phys-chem properties

Enumeration
● new editor interface
○ key issue: 1 canvas is not enough
○ edit parts of the Markush structure in separate editors
○ structure issues can be isolated to pieces
○ works well with small and large libraries
● interactive preview of enumerated structures

Searching
● full coverage of JChem search options
● default Standardizer config included
● easy access to virtual screening
○ structural similarity
○ pharmacophore similarity
○ close analog searching and scaffold hopping
● includes Marvin for JavaScript, our new
lightweight editor
● UI reworked to split basic and advanced options

Details view
● form view
● Calculator Plugins
○ structures with incremental result values
○ property lists
○ charts

Current coverage
● Document to Structure
● JChem Base
● Standardizer
● Markush Enumeration
● Calculator Plugins
● Screen
● Marvin Applet, Marvin for JavaScript

Roadmap
● project and user management
● virtual synthesis with Reactor
● clustering with JKlustor
● data visualization

As scientists we need to deal with inordinate amounts of data every day: we generate, retrieve and manipulate new data as part of our job. Simple excel worksheets are not the solution in the modern era of drug discovery, development and beyond. In this session learn how you can use and integrate ChemAxon’s tools to solve your day-by-day tasks more quickly and efficiently. Whether you prefer a desktop, web-based or touch screen application, we have a solution. Learn how to manipulate your data using Instant JChem (on your desktop or via Web layer) or draw sophisticated queries using Marvin or our new addition Marvin for Java Script (Marvin JS) to reduce the search times, visualize your data in 3D using Marvin Space, export and explore chemistry with the Ubiquitous Excel using the JChem for Excel plugin and share ideas and data with you colleagues and/or collaborators using Crais Board. Integrate our tools in Pipeline Pilot and Knime protocols and generate new data to expedite your processes. Analyze your data using Spotfire through Instant JChem. Also learn how our newest addition, Plexus, will help you do you tasks on desktop using web technology.

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EUGM 2013 - Gabor Guta (ChemAxon) - JChem Web Services

ChemAxon

We introduce the all new JChem Web Services platform that allows universal access to ChemAxon’s drug discovery platforms and offers true flexibility with its brand new RESTful API. A fresh take on the existing toolkits allows users to create and integrate applications with high productivity from any programming language, including C/C++, Python and Javascript for any platform including PC, Mac, Android and iOS. We demonstrate the capabilities through examples, including the all new ChemAxon Plexus web application.

EUGM 2013 - Roland Knispel (ChemAxon) - Biologics at ChemAxon From Old Powerh...

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Biologics have become an integral part of the drug development cycle within the pharmaceutical industry. But current cheminformatics toolkits are not well-suited to facilitate representation and computational interrogation of large biomolecules in the same way as for small molecules. Our Marvin suite is the product most frequently exposed to our users, and with recent releases, we aimed to continuously improve support for its application in a biopharmaceutical setting. But where these improvements are a mere extension of our classical cheminformatics tools, we have taken up development of a novel Biomolecule toolkit in parallel. It shall address the identified shortcomings in the data handling of large biomolecules with full atomic description, comparison of large biomolecules, and the exposure of distinct data views for different specialty groups of scientists. In this short presentation we will outline our future roadmap in the biological sector.

EUGM 2013 - David Deng, Daniel Bonniot (ChemAxon) - What’s New with Naming

ChemAxon

ChemAxon’s Naming provides reliable English name and chemical structure conversion. It is the underlying technology utilized in ChemAxon’s chemical text mining tool D2S (Document-to-Structure), JChem for SharePoint, and Chemicalize.org. In this presentation, the latest enhancement will be highlighted, including: Chinese chemical name recognition to accommodate the fast grouping Chinese scientific literature, Custom corporate ID to structure conversion using a webservice, Database indexing of structures from document repositories.

EUGM 2013 - Anh Kiet Tran Minh (CNRS): French Academic Compound Library: the ...

ChemAxon

Created in september 2003, the “Chimiothèque Nationale” (CN) – French Academic Compound Library – has for mission to federate collections of synthesis products, natural compounds and natural extracts available in French academic laboratories and to promote their scientific and industrial valorisation. Information concerning available molecules and extracts are contained in two databases (synthesis products, natural compounds and natural extracts), accessible through a web portal (http://www.chimiotheque-nationale.org/). The compounds database currently refers about 50,000 molecules coming from 30 French academic laboratories. The chemical compound database is built on Oracle database and IDBS tools (ActivityBase and ChemXtra). Chemaxon tools are also integrated in the CN information system : Marvin applet and calculator plugins. For several reasons (including software maintenance costs and evolutivity), we decided recently to evaluate the possibility to move to Chemaxon tools (Jchem, Jchem Cartridge and Standardizer). I will show you the present and future (expected) use of Chemaxon tools in the CN information system.

EUGM 2013 - Eufrozina Hoffmann (ChemAxon): Marvin extending the scope of usab...

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The Marvin package consists of applications for drawing and visualization of chemical structures and reactions. We will focus on the main features of MarvinSketch version 6.0 giving special attention to structure drawing, displaying and usability improvements. To finish we will be looking at the new member of the package: Marvin for JavaScript, which we will introduce as an easily integrable web component for 2D sketching and basic rendering.

EUGM 2013 - Odon Farkas (Eotvos University) - Conformation search via cool dy...

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The present method is the basis of the developing Conformation Plugin, a new calculator tool in Marvin. Our method is not one of the usual conformer search techniques, as it uses a new molecular dynamics method to directly provide ready-to-use low energy conformations. The advantage of conformation search instead of optimizing conformers, when one is looking for bioactive conformations, is shown. We present the highlights of the algorithm and comparisons based on data published recently.

Pre-clinical drug discovery strategies include target-based and phenotypic screening, natural substance modifications and biologic approaches. To demonstrate how cheminformatics approaches contributed to the discovery of new medicines we analysed recently approved drugs. In this presentations, we place ChemAxon’s Discovery toolkit in this context and demonstrate possible applications for 2D and 3D similarity studies, high-throughput pairwise molecular alignments or scaffold hopping. Moreover, we also discuss the technological challenges and realization of such applications in corporate platforms.

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EUGM 2013 - Attila Szabo (ChemAxon) - Collaborate and search in SharePoint wi...

ChemAxon

Microsoft SharePoint is a widely used web-based collaboration platform, which enhances internal communication opportunities between working teams at different locations. ChemAxon’s extensions enable chemistry under the SharePoint platform by integrating JChem and Marvin. This presentation will show you how to leverage the structure drawing, handling and searching capabilities in a collaborative environment as well as highlight the new developments, including previewing search results.

EUGM 2013 - Sergio H. Rotstein (Pfizer): What about the “big guys”? The emerg...

ChemAxon

The recent increase in utilization of complex macromolecules such as Antibody-Drug Conjugates (ADCs) as therapeutic agents has revealed a substantial gap in the biopharmaceutical industry’s portfolio of informatics tools and methods, most of which were designed to work primarily with either small molecules or unmodified and unconjugated amino acid and nucleotide sequences. The Hierarchical Editing Language for Macromolecules (HELM), along with a software toolkit that leverages that language was developed by Pfizer researchers to address this gap (see J. Chem. Inf. Model 2012, 52, 2796-2806). HELM and related technologies such as SCSR (Self-Contained Sequence Representation, see: JChem Inf Model. 2011 51, 2186-208.), enable the representation of unnatural, conjugated or otherwise modified building blocks in biopolymers such as oligonucleotides, peptides, proteins and ADCs. HELM is being released into the Open Source and the Pistoia Alliance has initiated a project that has the goals of (1) facilitating this release, (2) adopting HELM as an industry standard for the manipulation and exchange of complex biomolecule data, and (3) setting up the organizational infrastructure to govern the future development of the standard. Given the recent FDA approval of the Antibody Drug Conjugate Kadcyla (Ado-Trastuzumab Emtansine) for Her2-Positive Metastatic Breast Cancer, one can reasonably assume that standards such as HELM and associated software tools will play an increasingly prominent role as part of the modern drug discovery informatics arsenal.

EUGM 2013 - Andrea de Souza (Broad Institute): Setting the stage for the “SD”...

ChemAxon

Building on the success of the Molecular Libraries Program (MLP), the Broad Institute MLP team is co-leading with the National Center for Advancing Translational Sciences (NCATS) an NIH-sponsored project across 7 institutions to augment the data in PubChem with the creation of the Bioassay Research Database (BARD). The BARD platform standardizes the representation of bioassays in a next-generation repository and provides a user-friendly interface that supports sophisticated queries and data mining. Data originating from publicly-funded chemical biology research efforts will be presented with appropriate context including structured assay and result annotations. These annotations use relevant ontologies including, for example, the BioAssay Ontology, Gene Ontology, and the Unit Ontology. We simplified the representation of ontologies into a hierarchical data dictionary to enable data producers to more easily create and upload projects, assays, and results, while creating two separate user interfaces for data consumers. The BARD WebQuery Interface leverages a Google-like interface with auto-suggest functionality for complex queries, such as retrieval of all assays, and results for biological pathways such as “DNA repair” or “oxidative stress”; presentation of this information in a rich-user interface that includes spreadsheet support for structure-activity relationship analyses. Compounds, projects, and assays can be exported into an Amazon-like query cart for refining queries, and additional computations can be executed on datasets via community-developed plug-ins including promiscuity analyses via the BioActivity Data Associative Promiscuity Pattern Learning Engine (BADAPPLE) and a CYP450 metabolism site prediction plugin (hgp://www.farma.ku.dk/smartcyp/) using 2D structure fingerprints. Integration between the WebQuery and Desktop clients enables power users to initiate analyses in WebQuery and gain more insight via the Desktop client. Lastly, as industry and academia work together to innovate in small-molecule therapeutics, we have created an initial specification for the Assay Definition Standard. This standard through the Assay Definition Format has been used as the medium of data file transfer for data upload. We expect that the Chemical Biology community now has an opportunity to leverage this standard to routinely transfer assay and result data within and between information systems and organizations. This presentation will highlight the BARD platform with a focus on representing the cumulative body of work that exploits the ChemAxon toolkit.

EUGM 2013 - Steve Hajkowski (Thomson Reuters): Patent analytics - what can Ma...

ChemAxon

EUGM 2013 - Peter Englert, Peter Kovacs (ChemAxon) - The Next Generation of M...

ChemAxon

Finding the maximum common substructure (MCS) among molecules has many applications in the field of cheminformatics. It can be used in automated reaction mapping and molecule alignment, and it is also a popular measure of similarity, just to name a few. However, the complexity of the problem makes finding the exact MCS of two molecules too time-consuming for most use cases. At ChemAxon, we employ approximation algorithms in MCS search, but building one which is both practically fast and accurate is still a challenge. To meet the increasing demands on effective MCS search, we have taken our previous approach and applied different heuristics to further improve its speed and accuracy. The results are very promising, both in large-scale tests involving thousands of different compounds, and in application-specific cases.

EUGM 2013 - Michael Dippolito (Deltasoft): Great Migrations! – Approaches to ...

ChemAxon

EUGM 2013 - Christopher Southan (TW2Informatics): Chemicalize.org, SureChemOp...

ChemAxon

The ChemAxon Name to Structure functionality is not only a component of the SureChem patent extraction pipeline but also powers chemicalize.org. Both operations are now submitting sources to PubChem. The former has deposited structures that bring the patent-extracted total in PubChem to 14.5 mill. CIDs. The deposition from chemicalize is ~0.3 mill., but has been actively selected by users and is 20% unique. The final conjunction is that all three sources generate the InChIKey that turns Google into a de facto merge of PubChem and ChemSpider of ~50 mill. structures. Chemicalize.org users can convert new patents, other external or internal documents and web based text. Individual results can be Googled, searched against SureChemOpen and bulk extractions triaged against PubChem. It thus becomes possible to connect chemistry between patents, papers, abstracts and database records via exact match or similarity searching. When SureChem and chemicalize.org update their submissions, relationships with the other 47 million structures from ~200 PubChem sources (including ChEMBL and vendor databases) are re-computed and new CID links made. The synergy between SureChem and chemicalize.org is powerful because matches between them (~ 0.15 mill.) via SureChemOpen, give occurrence statistics and the location of the structure within patents. The applications of chemicalize.org are extended by web tools such as Venny for determining intersects from multiple extractions and CheS-Mapper for cluster visualization. These utility expansions will be illustrated by documents specifying BACE1 inhibitors for Alzheimer’s disease.

EUGM 2013 - Björn Windshügel (European ScreeningPort): Chemoinformatic tools ...

ChemAxon

In the drug discovery process high-throughput screening is often applied as initial procedure for the identification of hit molecules against a certain target, e.g. an enzyme or G protein-coupled receptor. In addition, virtual screening campaigns utilizing commercially available compound libraries are often performed that allow the search for potential hit molecules within a much larger chemical space as usually accessible within the in-house compound libraries. Chemoinformatic tools provide the opportunity to assist in the setup of experimental and virtual screening campaigns (e.g. assembly of compound libraries) as well as the analysis of screening results and structures of hit compounds. In this presentation the implementation of ChemAxon tools into the European ScreeningPort workflow will be presented using selected examples from previous and ongoing experimental and virtual screening campaigns.

EUGM 2013 - Gyorgy Pirok (ChemAxon) - Prediction of Xenobiotic Metabolism

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Metabolizer is a new tool from ChemAxon to predict and rank the metabolites of drugs and xenobiotics. Metabolizer contains a built-in library of human biotransformation schemes which were collected from literature although users can also add their own library to customize the calculation. The presentation will include insight to some technical details, initial results and statistics, explanation of the key metabolic indicators, and the method of major metabolite identification.

EUGM 2013 - Ian Berry, Bob Marmon (Evotec): Classification and analysis of 21...

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EUGM 2013 - Bernd Rupp (FMP) Chemical Information systems: From compound coll...

ChemAxon

The FMP has developed a database of commercially available compounds which is used to design our in-house HTS collection and is additionally applied to create focused libraries. But the dramatically increase of unique compounds of one order of magnitude from less than 10 to around 30 to 40 million compounds currently and approximately hundred million compounds in the next years requires a reorganization and redevelopment of our storage and searching strategy. To manage such a massive amount of data we developed a Registration Database for registration and normalisation of vendor catalogues. This database contains the highly redundant data of the vendor catalogues and is converted in a second step into the non-redundant Unique Structure Database which represents a data warehouse combining vendor data, structural descriptors and in-house classification tools including our earlier developed ADMET- and reactivity filters as well as our in-house fragment-based fingerprints used for library design tasks. The management of both database systems is part of a new developed Java application, which handles the user management for the data upload in the Registration Database and the conversion into the Unique Structure Database. Further a first version of a Web service is in preparation. This service allows the scientist not only to search for compounds and fragments in the Unique Structure Database but also to combine such a search with the FMP tools to classify compounds for their usability in biological assays.

EUGM 2013 - Anna Tomin (ChemAxon) - Reaction Library Design

ChemAxon

ChemAxon’s Reaction Library provides a full spectrum of organic chemical reactions used in synthetic routes from recent chemical literature. It incorporates both experimental and in-silico transformation rules to help chemists explore chemical space. Reactor provides a wizard-like interface to generate products without minimal manual interference. However, users are also provided with full control over the reaction rules, and they are able to implement their own reactions easily. The presentation will highlight chemical features as well as design and application of our diverse reaction collection in Reactor.

EUGM 2013 - Timea Polgar (ChemAxon) - 3D visualization for medicinal chemists

ChemAxon

Open Chemistry, JupyterLab and data: Reproducible quantum chemistry

Marcus Hanwell

The Open Chemistry project is developing an ambitious platform to facilitate reproducible quantum chemistry workflows by integrating the best of breed open source projects currently available in a cohesive platform with extensions specific to the needs of quantum chemistry. The core of the project is a Python-based data server capable of storing metadata, executing quantum chemistry calculations, and processing the output. The platform exposes RESTful endpoints using programming language agnostic web endpoints, and uses Linux container technology to package quantum codes that are often difficult to build. The Jupyter project has been leveraged as a web-based frontend offering reproducibility as a core principle. This has been coupled with the data server to initiate quantum chemistry calculations, cache results, make them searchable, and even visualize the results within a modern browser environment. The Avogadro libraries have been reused for visualization workflows, coupled with Open Babel for file translation, and examples of the use of NWChem and Psi4 will be demonstrated. The core of the platform is developed upon JSON data standards, and encouraging the wider adoption of JSON/HDF5 as the principle storage mediums. A single page web application using React at its core will be shown for sharing simple views of data output, and linking to the Jupyter notebooks that documents how they were made. Command line tools and links to the Avogadro graphical interface will be shown demonstrating capabilities from web through to desktop.

USUGM 2014 - Erin Bolstad (ChemAxon): Consultancy report - New capabilities a...

ChemAxon

ChemAxon’s consulting services has undergone substantial growth in the last several years. We now utilize talent from across the globe, servicing a wide range of project needs. From small short term solutions to mega-pharma project management, small-scale software integration/migration to customized product development. This presentation will cover some of the range of projects we are engaged in with some focus on a large web portal project we delivered for the European Lead Factory.

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