An opportunity for all attendees of the training sessions and UGM to talk face to face with our development team in an informal environment. Bring your detailed questions and issues, learn about development roadmaps, present your suggestions and ideas. The One-2-One session will be followed by an informal social program.

We use open partnering to describe the way we communicate with all our partners – where open equals our transparency in business and development modeling and partnering means our clients and listening, taking on board ideas, joint projects, industry relevance as the field progresses. We will highlight our first 12 years, our current emergence and how it relies on open partnering for us to become the partner of choice in established sectors like platform IT and in emerging areas like MCS clustering and adoption of SharePoint or innovation as with our Markush structure handling.

The back-end (chemical engine) products of ChemAxon will be introduced with special focus on latest developments. JChem Base is a chemical database management toolkit to handle molecules, chemical reactions and Markush structures and associated data stored in relational databases. JChem Cartridge provides similar functionality highly integrated into Oracle as well as an SQL interface to other ChemAxon products.

The Chemical Biology Platform at the Broad Institute builds a wide array of tools to support its activities as a Comprehensive Center for the Molecular Libraries Probe Production Centers Network (MLPCN). After a comprehensive review of all current commercial and open source offerings, we elected to migrate our chemical toolkit from existing Daylight to ChemAxon technology. Our goal for the migration was to minimize the impact on the data as we provided users with improved and additional functionality. We identified core functionality that required modification, prototyped the functionality, reprocessed all relevant chemical data, and evaluated chemical differences with the user community. Iterative development coupled with critical review for chemical differences with Instant JChem, resulted in a successful migration with additional enhancements for our users. This presentation describes the type of functionality migrated, the Instant JChem review tool created and our lessons learned. In addition, some user facing enhancements enabled by Chem Axon for compound registration will be discussed.

Library enumeration is a powerful way for the generation libraries containing loads of NON-synthesizable compounds. At least not on that planned synthetic route due to activation/deactivation issues, directing rules and side reactions. The design of virtual reactions will be demonstrated via step-by-step examples: sketching generic reaction scheme, examination of the foreseeable synthetic problems, finding out and formulating solutions to get reusable reactions producing synthetically feasible compounds.

This session will include brief presentations from ChemAxon’s partners. For the details please come back later.

Microsoft SharePoint Server is becoming the standard portal platform at most major pharmaceutical companies. It lets scientists to easily share and manage research and discovery data. Most of the information in an organization resides in unstructured data. Use JChem Search for SharePoint to index and find chemical entities within documents on file shares, e-mails, pages from the Internet or corporate intranet. ChemAxon’s SharePoint extensions enable chemistry inside SharePoint not only on the enterprise, but also at the individual level. Manage and filter for structures inside lists, wikis, blogs and discussion boards. Custom calculation field type allows to display structural property predictions in lists. Import from, and export to various chemical file formats.

The first evening of the UGM will host our usual Grand Dinner. This time we’ll have a dinner in the Harvard Faculty Club. Buses will leave the event hotel at 6:30 pm and reach Cambridge by 7 pm. Transportation will be provided after the dinner too – buses will leave the club at 10:30 pm. Do not hesitate to join us!

This talk covers GSK R&D IT’s current progress in leveraging Service Oriented Architecture (SOA) against the problems posed by a mixed technology environment. During 2009 and 2010 IT has undergone a push to simplify the architecture, technologies and vendors used in order to reduce the cost of on-going support and maintenance of our vast application portfolio. One solution has been to consolidate the number of vendors used and to standardise on a suite of webservices that can provide the required functionality. ChemAxon was chosen to provide a number of the generic chemistry functions used by Discovery IT, ranging from structural searching to 2D rendering. We will begin by discussing how the ChemAxon toolkit and cartridge has been integrated into the enterprise environment and detail the effort required to migrate from some existing vendors to ChemAxon. We will also discuss the advantage SOA has played in this migration with respect to cost and client applications. Finally, we will show details of how the ChemAxon product has evolved in our systems and led to gains in consistency and supportability.

ZINC is a free database of commercially available compounds for virtual screening, available on the web at zinc.docking.org. We have implemented a free public search of 32 million purchasable molecules using ChemAxon tools. This presentation will describe our implementation and demonstrate its use for some common and not so common tasks, focusing on SAR by catalog.

The ChemAxon Markush project includes drawing, visualization and generation of Markush structures, Markush enumeration techniques and searching. The generic notation includes R-groups, atom and bond lists, link nodes, repeating groups, position variation and homology groups. The project reached a milestone: Markush structures from Thomson Reuters’ MMS(Merged Markush Service) database can now be handled via the Markush DARC file format (.VMN). It will be shown how the contents of this Markush patent database is handled, and recent and near future developments will be introduced.

We will describe how we are using IJC across chemistry and biology to link data for many of our customers projects

GSK Has developed a user tool for SAR analysis based on JChem for EXCEL integrated with our SOA architecture based on ChemAxon technology. The tool provides a seamless interface that allows GSK researchers to retrieve structural, chemicophysical and biological data into the ubiquitous EXCEL spreadsheet, providing extensive flexibility during SAR exploration.

Tautomerism is an important and difficult problem in cheminformatics, and has gained much attention recently. [1] The presentation will focus on ChemAxon’s approaches and algorithms for handling tautomerism. There are four main topics to cover: 1. The tautomerization calculator plugin [2] is the basis of most methods. It can identify tautomerizable regions, enumerate all or dominant tautomers and predict the distribution of dominant tautomers. Furthermore, it can provide generic and canonical tautomers that are used by the methods discussed. It first identifies possible proton donors and acceptors and finds the tautomerization paths between them. Depending on the desired operation, it then combines the paths into regions (generic tautomer), combinatorially enumerates all possible tautomeric forms (all tautomers), filters and ranks enumerated structures based on pKa and other criteria (dominant tautomers) or canonicalizes using empirical rules (canonical tautomer). The tautomerization plugin is also used to improve results of other calculations, such as macro pKa and logP. 2. Tautomer duplicate search uses generic tautomers combined with a hash key. This method also allows fast filtering of tautomers in chemical database tables. It will be shown how this method is able to handle tautomeric migration of H isotopes and interactions with stereochemistry. 3. Tautomer substructure search enumerates tautomers of the query, and searches each of them separately. In case of query H constraints (explicit H), the constraint is enforced on the tautomeric region to retrieve only true tautomers. 4. Standardizer is a tool for performing custom and built-in transformations on molecules. It is integrated with the JChem chemical database system, so that database and query structures are automatically transformed by the specified transformations [3]. It will be shown how the canonical tautomer and custom transformations can be used to handle tautomerism. Custom transformations also allow handling of ring-chain tautomerism. References: [1] Martin, Y.C.: Let’s not forget tautomers J Comput Aided Mol Des (2009) 23:693–704, DOI 10.1007/s10822-009-9303-2 [2] Szegezdi, J.; Csizmadia, F: Tautomer generation. pKa based dominance conditions for generating dominant tautomers. American Chemical Society meeting, Aug 19-23rd, 2007 http://www.chemaxon.com/conf/Tautomer_generation_A4.pdf [3] Pirok, G. et al: Standardizer – Molecular Cosmetics for Chemoinformatics. Drug Discovery Technology, August 7-10th, 2006 http://www.chemaxon.com/conf/standardizer.pdf

We will present improvements in our name to structure and structure to name tools. We also demonstrate the extraction of chemical structure from their names occurring in text documents, with PDF format support in addition to already supported text and xml/html. We present the new version of the chemicalize.org website, with chemical name highlighting, rich molecule property calculations page and structure search on more than a hundred thousand indexed web pages.

To be announced.

Open discussion about Markush structures for IP and CombiChem. For more details please visit the forum’s page.