Monday, 26th Sept afternoon -Markush Forum, a meeting for those who are interested in the development of ChemAxon’s Markush structure enumeration and search tools and the available content.
Tuesday & Wednesday, 27th-28th Sept - The UGM will include presentations from ChemAxon users, partners and developers with opportunity to network with peers and meet with developers.
Thursday, 29th Sept - Following the UGM program we host the training day that consists of two parallel tracks. The developers' training deals with technical questions, the Application focus training introduces ChemAxon products to end users.
Plenty of opportunities for networking
Speaking to peers and colleagues in addition to the lunches and breaks we have organized social programs to keep the ideas flowing.
Sunday: informal gathering in the bar of the event hotel from 7 pm. Monday: chat and dinner in The BeachWood Tuesday: Gala Dinner in San Diego downtown, in the Stingaree Wednesday: chat and dinner in the Pacific Beach Bar & Grill
Markush Forum
Monday September 26th afternoon, preceding the UGM San Diego. The Markush Forum provides an opportunity for interested organizations to participate in the further development of ChemAxon’s Markush tools for IP search.
Thursday September 29th, the UGM will be followed by a dedicated Training day with two parallel tracks: one for developers and one for end users. The main goal of our technical training is to introduce the new product features and give answers to the questions of how ChemAxon tools can be best integrated in various cheminformatics applications.
Thursday September 29th, the UGM will be followed by a dedicated Training day with two parallel tracks: one for end users and one for developers. The aim of our Application focus training is to give end users and those new to ChemAxon a handle on basic ChemAxon functionality and how you can interact with it.
In the first break of the UGM we will host our traditional one-to-one session, where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group will have a discussion table in the break room.
For more details on the topics of the 1-2-1 session visit this link.
ChemAxon Partner participation
Partners' lightning round presentations On Tuesday, 27th of September, from 2 pm a one and a half hour session will be dedicated for ChemAxon Partners who will give brief overviews of how ChemAxon works within their products and services.
Partners' table-top exhibition Throughout Tuesday and Wednesday, partners will be available at exhibition sessions where attendees can meet and find out more about partner products and services.
For more details on partners' participation please contact Nóra Lapusnyik.
Contact us
If you have any questions, comments or requirements about the ChemAxon UGM feel free to contact János Fejérvári.
Costs
The cost of the 2 day User Group Meeting is $400 for corporate attendees and $200 for academics.
For the training day (either/both tracks) the costs are $550 for corporate attendees and $275 for academics. Training attendees can attend either track. The fee for the training day does not include the user group meeting fee.
The cost includes all breaks, lunches and the social programs and all attendees will receive upon payment an evaluation license for all products valid for one month after the event.
We look forward to welcoming you in September.
Accomodation
The Catamaran San Diego Hotel, Spa and Resort will host our UGM in San Diego. Note that the hotel tends to be full soon, so please proceed with your room reservation.
The web interface of the ZINC database (ZINC Is Not Commercial) has been redesigned to simplify the process of finding commercially available small molecules of biological interest and then organizing and prioritizing these compounds for purchase. Perhaps the single most significant feature is the use of a shopping cart metaphor to organize and manage results over the life of a project. This talk presents four common use cases: A) starting from a single molecule, identify analogs; B) starting from a single molecular target, identify purchasable annotated compounds, purchasable analogs of these, or purchasable predicted compound; C) starting from a set of actives, perform SAR by catalog and prioritize the results; D) starting from docking results, prioritize the best compounds for purchase. Until its release in the fall of 2011, this new ZINC interface is available at http://zinc12.docking.org/
GSK has, over the last several year, taken an aggressive look at cost control in the IT area. Many IT systems and processes have been revamped in an effort to reduce cost. One of those efforts targeted our chemistry cartridge implementation and associated systems. The cartridge that was the prior GSK standard required a large maintenance spend and the technology was not moving forward. After performing a market evaluation GSK made the move to JChem. In making this choice, the GSK Registration system was also targeted for replacement since the application was based on the previous technology.
Not only was the registration system to be replaced, but the process needed re-engineering itself. Cuts in staffing reduced the number of registrar significantly from 5 FTEs to 2 FTEs. With the previous system, the registrars were the Quality Assurance administrators of the registry data. They ensured that standards were met for all aspects of registry representations. The teams challenge was to develop and implement a JChem based registration system in conjunction with ChemAxon, that would allow the quality of the registered data to be maintained while reducing the registrar support needed to curate. Some of this “QA” burden needed to be pushed back to the chemists synthesizing the compounds.
The GSK teams second challenge was to select an implementation that would “fit” with the reductions in support staff that came with GSKs cost cutting measures. In order to address this issue, GSK and ChemAxon have designed a novel approach to Software as a Service that allows protection of GSKs IP investment, but still lets the software management and support be “owned” by ChemAxon. This presentation will summarize our progress, some of the issues that we have encountered and plans for the system in the future.
Registration is an important part of any company dealing with chemical compounds. In this presentation, we will describe the features of this upcoming product and display screen shots of the client interfaces. After providing a basic understanding of the architecture and workflow of a submission, we will tell you what is configurable in the system and how this product can fit into your company’s environment.
RTI International has implemented a robust cheminformatics solution based on ChemAxon’s chemistry tools and DeltaSoft’s web applications to facilitate chemical space/chemometric/bioassay property mining of over 50‐years of Medicinal Chemistry/Pharmacology data. Our ChemCart Registration, ELN, BioAssay, and Structure‐Activity applications are powered by the Marvin and JChem Cartridge chemistry engines. With this system, researchers can register, search, and browse chemical structures with related test result data (including files and images). Furthermore, the implementation allows seamless communication across the collaboration groups at RTI, while at the same time providing secure ‘data vaults’ for non‐collaborative information. The manner in which fine‐grained security has been implemented while maximizing access to ChemAxon computed properties will be described in detail.
Chemical structures often suffer from various drawing errors. These errors may originate from actual drawing mistakes, or insufficient structure recognition and interpretation of structure images. Also, in case of old structural databases the limitations of early technologies may lead to inconsistent chemical structures. Structure Checker is capable of recognizing, reporting or automatically fixing most of the structural errors in chemical structure representations, which makes it a key component for chemical registration systems. The usage and configuration of the reporting and fixing features will be presented using selected examples.
The Chemical Biology Platform within the Broad Institute screens both the Molecular Libraries Small Molecule Repository (MLSMR) and a unique compound collection synthesized internally through diversity oriented synthesis, yielding novel starting points for follow-up chemistry in a range of disease areas including cancer, diabetes, and psychiatric illnesses. The supporting informatics needs include sample tracking, analysis of high-throughput assay data, hit evaluation, and analysis of compounds by patterns of activity across multiple assays (e.g., to understand mechanism of action). Data and results have been made public first through ChemBank and subsequently through PubChem and CARS. As our focus has shifted from infrastructure development to supporting the discovery of putative novel therapeutics, our informatics requirements now include capture of the entire discovery life cycle (assay development, HTS, lead optimization, ADME etc.).
This presentation describes the evolving informatics needs relative to probe and drug discovery. It includes an overview of informatics initiatives with a focus on our current Chemical Biology Informatics Platform (CBIP), and our plans to evolve toward a modular system that enables biologists, chemists, and computational scientists to integrate chemical and biological data. Success stories that highlight the ChemAxon family of products since the transition from a legacy chemistry cartridge in March 2010 will be presented including how we have integrated ChemAxon into our environment over the past year-and-a-half: hit calling for high-throughput screens, cherry picking of compounds for retest, and stereo-structure-activity relationship analysis.
Reagent logistics is a key process to enable drug discovery research. The information systems that facilitate this process allow scientists to identify, procure and track reagent samples. We have developed two web‐based systems, Chemical Requisition System (CRQ) and Chemical Inventory System (CIS), that are integrated into our Enterprise Resource Planning (ERP) System. Utilizing these tools, scientists are able to query chemical reagent repositories using JChem Base/Cartridge and complete execution of operational logistics tasks (e.g. barcoding, disposing, check out/in).
The Core Laboratory for Neuromolecular Production at the University of Montana is applying a variety of chemoinformatic approaches to the integration of research across several neuroscience drug‐design groups. These groups span a variety of targets affiliated with important disease states, such as Parkinson’s, Alzheimer’s, ischemic stroke, and neuropathic pain. Central to this approach has been ChemAxon’s diverse tool set for database mining, pharmacophore development, high‐throughput screening, and diversification of current and new leads. Here we report on the latest developments of our ChemAxon based system.
This talk will detail the latest and future developments in the JChem server products: JChem Base, Cartridge, Web Services and Markush search. The new molecular formula search types will be described, as well as the huge performance enhancements in R‐group searching and various other news like similarity hit display, new stereo types support, jcunique application, etc. Markush searching introduces better support for combinatorial Markush structures (allowing thousands of R‐group definitions), new query features including R‐group queries, translation options, atom properties and GUI improvements in Instant JChem. The new Markush Viewer application allows a static, but effective overview and navigation of Markush structures. A quick glimpse will also be provided for ongoing developments including grid support, Markush search and enumeration speedups and efficient drug‐like filtering capabilities for Markush enumeration.
Life scientists have found Microsoft Excel to be an invaluable tool in managing and visualizing research data. ChemAxon’s JChem for Excel (JC4XL) enhances Excel’s capabilities by including cheminformatics features. This presentation will highlight deployment of JC4XL in a dynamic IT and Informatics environment with limited resources. Additionally, JChem for Excel integration into proprietary tools will be discussed and presented.
Instant JChem 5.4 included many new ways to view and work with data. New form widgets provide ways to generate information rich forms, and to visualise data graphically, and interact with it. This provides a simple but powerful environment for the medicinal chemist. We will show examples of how this can be used as part of a combinatorial library design package where a library is built and analysed within an Instant JChem database.
GSK are in the process of migrating from its legacy forms‐based SAR software to Instant JChem. Ultimately the goal is to see a multi‐tiered architectural solution, though Instant JChem in its current form is still much closer to its standalone desktop application roots. Working closely with ChemAxon, we have addressed the challenges of converting, securing, and tuning the performance of around 200 projects, then making the projects available to all departments from a single location. GSK have implemented some temporary solutions to overcome issues of network latency, but we expect to eliminate those stopgaps as ChemAxon make strides toward reducing IJC’s application schema overhead, improving search result browsing performance, and supporting virtualized data.
Starting with a brief overview of the chemistry Excel Add‐Ins available on the market, we will look at the migration challenges from these products. Using two real life case studies, we would like to illustrate how ChemAxon could help along the way, tailoring the product to your needs. Finally we see, through our plans and ideas, how far an Excel Add‐In could be enhanced.
Commercial add‐in programs introduce chemical intelligence into Excel, therefore enable Excel to become a serious development platform candidate for Cheminformatics applications. We will illustrate how the add‐in idea can be further extended to integrate Excel with the rest of the Cheminformatics infrastructure we have constructed over the years.
The use of SMARTS patterns for pattern matching has become ubiquitous in cheminformatics, and efficient implementations exist for identifying one or more instances of a user-defined substructure in a molecular graph. However, a very common usage of this functionality is in applications that test a number of patterns against each molecule. Examples include filtering of desirable/undesirable properties, atom typing, descriptor and physical property calculation, pharmacophore perception, feature-based fingerprint generation and IUPAC name generation. In these use-cases, current practice is typically to match each of the (SMARTS) patterns independently and sequentially.
This work describes significantly more efficient algorithms for matching multiple patterns simultaneously. Much like chemical database search systems use fingerprint pre-screens to optimize searching a single pattern against multiple molecules; pre-processing analysis and pattern compilation can be used to optimize matching multiple patterns against a single target molecule. The process takes a set of patterns and generates a Java class that performs this matching using the ChemAxon toolkit. This approach, which often makes the match run-time independent of the number of patterns, enabling software applications that require matching of thousands or tens of thousands of patterns.
Performance figures will be presented that show using these methods with the ChemAxon toolkits significantly improve real world applications, such as generation of 166-bit MACCS keys, over traditional sequential methods. Possible applications to patent indexing and searching will also be discussed.
JChem SharePoint is finally here. It has many building blocks allowing users to integrate chemistry functionality under SharePoint 2007 and 2010. We will briefly demonstrate the features, the planned enhancements and finally do a quick question and answer session with those interested.
Patents allow you a limited monopoly on your invention. Equally important, they allow your competitors the same monopoly on their inventions. Chemical structures in patents are frequently described in broad terms called Markush structures. This talk will describe some of the typical Markush structure searches of chemical patents, which are used to determine ‐ structures that are covered by many patents versus the “white space”; ‐ drug candidates structures that are not in the scope of the patented Markushes but are likely to have the same properties; ‐ whether an invention is patentable; ‐ whether you might have freedom to operate; or ‐ whether a third party’s patents are valid or can be “busted”.
Features and applications for IP challenges – working with ChemAxon Markush technology ChemAxon and Thomson Reuters have recently concluded a partnership to enable storage and search and advanced visualization of Thomson Reuters content, involving the Merged Markush Service (MMS) database, in relation to the Derwent World Patent Index (DWPI) and Derwent Chemistry Resource (DCR). An analysis of ChemAxon’s Markush selective and random enumeration and search capabilities is presented using the Instant JChem desktop application, running in the cloud and a custom interactive Markush structure browser. The analysis is illustrated by reference to specific examples, and provides detailed comments under the broad headings of database content, system, reduction of Markush structures, hit alignment and coloring.
Medicinal chemists rely on patent intelligence at three distinct junctures of a research project: inception of an idea, ongoing competitive intelligence during project development, and preparation of the patent application. Typically, a medicinal chemist collaborates with expert information scientists and patent attorneys to evaluate competitor’s intellectual property in order to assess where drug design efforts should be focused. The availability of comprehensive databases of exemplified and Markush structures make it feasible for medicinal chemists to carryout preliminary IP analyses on their own. The search capabilities of these databases generally are limited to substructure and similarity comparisons and few tools exist to fully evaluate and visualize the chemical space disclosed within a patent. To address the need for better IP analysis tools, Pfizer has developed a suite of patent analysis tools and made these available to medicinal chemists throughout the research organization. In addition to performing substructure, similarity and exact match searching against databases of exemplified structures from
patents, two of these tools compare structures based on an overlay of their reduced graph representations to facilitate analysis and visualization of the chemical fragments within a set of exemplified structures, and rank order a set of patents by structural relevance to one or more query molecules. Lastly, a Markush tool has been developed to facilitate analysis of the detailed chemical space disclosed within a patent. Using this tool, medicinal chemists can perform substructure and exact match searches against Markush structures from patents of interest and enumerate representative structures from the search hits.
Enumeration of compound libraries using virtual reactions is a powerful tool in the early phase of drug design. Through selected examples this presentation will highlight the novel features of Reactor, ChemAxon’s reaction enumeration tool. Among others, these features include direct editing of the reactants through Reactor’s graphical user interface, manual selection of main products of the enumerated libraries, or setting up reactant’s ratio. These extensions allow researchers – besides applying Reactor’s smart reaction rules – to grab full control over the fine tuning of the reaction enumeration process. Also synthesis code generation and usage will be demonstrated through real life examples.
Reaction scheme is a common form to illustrate synthesis planning and execution. It will be ideal to capture the information as it is. Yet, a system should be able to iterate the compounds in the scheme and possibly parse the scheme into individual reactions.
Among ligand-based virtual screening methods shape-based, ligand-centric approaches have shown promise in pharmaceutical drug design. Numerous comparisons of similarity methods were conducted using various data sets during the past few years. Here, ChemAxon 3D ligand-based approaches are validated on several targets from ChEMBL database. Evaluation of virtual screening results shows effectiveness of new screening methodology and good actives recovery rates.
Molecular fragments are ubiquitous in both experimental and computational chemistry. In many ways, fragments can be considered to be the n-grams of chemistry, allowing us to capture and explore structure-activity trends in large chemical collections. In this talk I will discuss how fragments play a key role in the analysis of HTS data at the NCTT as well as how we make use of fragments to explore bioactivity data across multiple targets and target families, focusing on the ChEMBL database. Some applications that I will discuss include searching for privileged substructures, series selection and R-group QSAR. We will present a standalone, freely available tool that allows users to explore ChEMBL using our fragment approach as well their own data using the same techniques.
Promiscuous compounds are associated with frequent hitters in HTS assays. We developed a method for rapid and automatic identification of chemotypes associated with frequent hitters based on matching molecular pairs concept. Using PubChem bioassay database we identified frequent hitters and “probable” chemotypes responsible for compound promiscuity. A scoring scheme was designed from distribution of biological activities across assays, substances, and molecular matching pairs, allowing for ranking of “most” promiscuous chemotypes. Identified promiscuous chemotypes can used as a filter for prioritization of HTS hits, and compound library design.
IUPAC, CAS, common, drug names form an important part of the chemical data generally available. We present the major upgrades to our name to structure which have been released in the last year, dramatically increasing the precision of the conversion. We also reflect on the possibilities in case of potentially ambiguous names, and the challenges of extracting names from documents, when some common names also have a non-chemical meaning.
As scientific and patent literature expands, we need more efficient ways to find and extract information. Text mining is already being used successfully to analyse sets of documents after they are found by structure search, in a two‐step process. Integrating name‐to‐structure and structure search directly within an interactive text mining system enables structure search to be mixed with linguistic constraints for more precise filtering. This talk will describe work done in partnership between ChemAxon and Linguamatics in the EU funded project, ChiKEL, including improvements made to name‐to‐structure software, how we evaluated this, and the approach taken to integrating name to structure within the text mining platform, I2E.
September 26th, informal lunch at 12:30 pm, session between 1:30 pm - 5:30 pm.
ChemAxon and Thomson Reuters have formed a partnership to enable storage, search and enumeration of Markush DARC format (VMN), which is used in Thomson Reuters’ Merged Markush Service database - interlinked with DWPI (Derwent World Patent Index) and DCR (Derwent Chemistry Resource).
The Markush Forum provides an opportunity for members of ChemAxon's Markush forum to meet and discuss developments and future directions with ChemAxon Markush search and enumeration technology working on Thomson Reuters MMS content.
Agenda of the Forum:
Intro from Thomson Reuters and ChemAxon
Review & discussion of user needs
Instant JChem Product demo
Thomson Reuters update on Markush data availability
How Thomson Reuters extract & create the Markush data
Overview of recent ChemAxon developments & roadmap
Discussion on future developments/priorities
Who should attend?
Information Managers, Patent information Specialists, Research Managers concerned with investigation of patent space, Patent Attorneys, Business Intelligence Analysts.
September 29th, approximately between 9:00 am - 4:15 pm. Runs concurrently with the Application Focus training day track.
The main goal of our technical training is to introduce the new product features and give answers to the questions of how ChemAxon tools can be best integrated in various cheminformatics applications
The training program will involve common problems, different concepts, the ChemAxon's Application Programming Interface (API) and examples to understand how to integrate ChemAxon’s components in discovery pipelines and custom applications. Common problems ranging from basic to more complex scenarios will be explored and solved by Marvin/JChem developers with interactive demonstrations.
Morning session
appr. 9:00 am - 12:15 pm - Introduction into ChemAxon's Marvin Suite
Structure representation, structure i/o, building molecules
Break
Marvin, basic and advanced programming, using applets and beans
Lunch
Afternoon session
appr. 1:00 pm - 4:15 pm - JChem solutions
Chemical database concepts, an introduction to JChem Base
Chemical database programming, examples of JChem Base API and JChem Oracle Cartridge usage
Break
JChem Web Services, introduction, concepts, live demo of worked examples
Closing remarks
101 FAQ's to be answered:
How are molecular structures represented with focus on implicit and explicit hydrogen atoms and stereo-chemistry?
How to build molecule from API?
What are the constituting components of a molecule, reaction?
How to read and write molecules in various file formats (SDF, Marvin document file)?
How MarvinView and MarvinSketch can be embedded in an HTML page?
How to embed Marvin in Swing components (JTable, JFileChooser)?
How Marvin can be customized in client applications: how to enable/disable tool bars, menu items; how to show/hide hydrogen atoms, labels?
How to generate images with Marvin?
How to add custom event handlers to Marvin applications?
How to add custom templates to the Template Library, or to Advanced Template Toolbar?
How to create editable molecular tables with MarvinView and MarvinSketch?
How to change the structure while transfering between the viewer and editor?
What tools does the Marvin library provide for other specific tasks?
How are structures stored in the JChem database?
How to search for molecular structures in chemical databases and how to sort hit lists?
What are the best approaches to visualize search hits?
How substructure search is sped up with the use of hashed chemical fingerprints?
How to fine tune and optimize structural searches?
How to standardize structures during compound registration and in hit visualization?
How to write web service clients in PHP, JavaScript, and Python to access JChem Web Services?
How JChem Web Services provides access to the JChem suite of tools? OR ... to your web applications?
How JChem Web Services uses SOAP to provide access to the JChem Suite of tools?
Application focus training
September 29th, approximately 9:00 am - 5:30 pm: Runs concurrently with Developer Training Day track
Application focus training is designed mainly for end users (chemists and biologists) and those new to ChemAxon, to get a handle on basic functionality and how you can interact with it. The morning session introduces key technologies and features, it introduces ChemAxon technology in general. The entire afternoon session is dedicated for hands-on training and workshops for advanced and new users too. For more details see the agenda below.
Since the training will have hands-on part you will need to bring your own laptop or let us know if you want to get a loaner for the training day. Also you will need to download and install the recommended software and licenses to your desktop (for the exact details please re-visit this page later). All attendees will get a free license valid for all ChemAxon products following payment until one month post event. To finish with registration and downloads in time we recommend to arrive at 8:00 am to the training.
Introduction to ChemAxon technologies
This lecture session is designed to introduce beginners or new users to the general capabilities of ChemAxon technologies, focusing on the most commonly used visualization techniques, chemical representations, property predictions, chemical databases and chemical database clients. It is also useful for current users who have not had the advantage of a structured introduction to the general functional expectations of ChemAxon technologies.
9:00 am - 10:30 am
Desktop technology
This lecture explains the usage of the technology built-in Marvin Suite. Sketching, visualization of molecules and reactions will be demonstrated. It will detail the concept and usability of some property calculations (e.g.: pKa calculations, conformation generation) demonstrating the Calculator plugin technology, moreover will discuss a new plugin technology that will enable users to integrate their own existing calculators easier.
This workshop session is designed to elaborate the morning session and provides hands-on experience for not only advanced users but beginners. Moreover, the workshops allow attendees to discuss and find solutions for their specific problems. The session is run in two tracks for desktop and enterprise solutions.
1:00 pm - 2:15 pm
Structure visualization and characterization
Basic, advanced features and latest improvements of Marvin are covered. Combining JChem for Excel functions and fine tuning visualization is discussed during this session.
2:30 pm - 4:30 pm
Enumeration technologies
Enumeration technologies enable users to generate virtual libraries based on generic reaction rules by Reactor or from Markush structures after drawing a generic reaction and a Markush structure using Instant JChem.
1:00 pm - 2:15 pm
Pipelining ChemAxon
This session covers the use of ChemAxon technology in Pipeline Pilot and Knime. Database management, property calculation, structure searching, similarity searching, reaction enumeration are covered.
2:30 pm - 4:30 pm
Instant JChem
Topics such as database management, hierarchical tables, form view design, standardization, structure checking, structure searching, Markush structure searching, Groovy scripting are covered.
