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.

1. The tautomerization calculator plugin 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. 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.

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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.

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Showing one example workflow for a focused library generation; the generated virtual library by Reactor will be further processed to find the most similar compounds to a given active set of compounds.

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This talk will follow-on to the presentation given by Brett Hiemenz at the 2009 US UGM which described the uses of a Service Oriented Architecture (SOA) and the problems faced in 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 standardise of a range of webservices that can provide the required functionality. ChemAxon was chosen to provide a number of these 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.

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SkunkWerks used JChem to provide substructure and similarity searches across an existing Screening Library System. The solution was integrated with the existing RIA applications and SkunkWerks proprietary back end. SkunkWerks opted for JChem’s Web Services as the means to communicate with JChem Base. Using JChem’s Web Services SkunkWerks was able to seamlessly integrate substructure/similarity searches into the application. This session will present the solution that was developed using JChem and Flex (Adobe Flex) for a RIA implementation.

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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. 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.

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.

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Please find out more about the session’s presentations in the Partner session tab.

We will describe the “fun” we are having creating rules and workflows to tidy up the data from chemical supplier catalogues for our compound sourcing database.

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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.

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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.

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Review features provided by the JChem for Excel API. How to integrate with existing Excel solutions in VBA, VSTO or COM Add-Ins. Look at how external applications could communicate with JChem for Excel, or read and write JChem for Excel specific workbooks using the Apache POI library.

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We provide examples of how a chemistry database can easily be created and deployed to users using Instant JChem. This will illustrate how the database can be built and incorporated into Instant JChem, and how forms can be built for the chemists to use to browse, query and manage the data. New features in Instant JChem that enhance this process will also be described.

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Both fragment counts and pharmacophore pattern fingerprints are classical, well-established molecular descriptors, thought to be complementary. The former provide a molecular skeleton-dependent encoding of the main substructures, while the latter capture information about relative spatial distributions of pharmacophore groups and are less focused on how these are interconnected (thus prone to successful lead hopping). We now set to explore hybrid intermediates of these two extreme classes of descriptors, such as pharmacophore fragments (substructures of the pharmacophore feature-colored molecular graph, having atom symbols replaced by their types) – all while benefitting from the pH-dependent flagging scheme achievable by means of the ChemAxon microspecies calculator. Alternatively, atom coloring by their partial charge, using the ChemAxon charge plugin, will be explored. Examples of usage of these descriptors in QSAR and similarity searches will be shown.

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Reference Space was defined by collecting known PDE inhibitors (“seeds”) from available literature and databases, and its property space was determined by applying the Lipinski and Veber parameters using InstantJChem. The searchable Chemical Space was composed by the recent edition of the 10 major vendor databases (cca. 10 M compounds). The ligand-based 2D similarity search (InstantJChem) was performed by setting a similarity treshhold (0.65-0.7 Tanimoto). The resulting set was shrinked to match the “reference property space” applying the appropriate physico-chemical parameter ranges. The filtered focused library was further analyzed to reach a reasonable diversity („seed” compound representation/ chemotype distribution) using InstantJChem and LibMCS and the process was completed by visual inspection. In the presentation we discuss our experience in the focused library generation and share the lessons we learnt during the application of the ChemAxon software family. This work was partially supported by the National Development Agency (NKÜ) grant: #KMOP 1.1.1-07/1-2008-0029) [1] Decornez H, Gulyás-Forró A, Papp A, Szabó M, Sármay G, Hajdú I, Cseh S, Dormán G, Kitchen DB Design, selection, and evaluation of a general kinase-focused library. ChemMedChem. 4(8), 1273-8 (2009). [2] A. Tovar, H. Eckert, J. Bajorath, Comparison of 2D Fingerprint Methods for Multiple-Template Similarity Searching on Compound Activity Classes of Increasing Structural Diversity, ChemMedChem, 2, 208-217 (2007).

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