Where and when? - ChemAxon's 8th European User Group Meeting will be held on Tuesday and Wednesday, May 22nd-23rd, at the Hotel Novotel Budapest Centrum.
Monday, 21st May afternoon -Markush Forum, a meeting for those who are interested in the development of ChemAxon’s Markush technology and the available content.
Tuesday & Wednesday, 22nd-23rd May - The UGM will include presentations from ChemAxon users, partners and developers with opportunity to network with peers and meet with developers.
Thursday, 24th May - Following the UGM program we host the training day that consists of two parallel tracks. The developers' training deals with technical issues, 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 hotel's bar. Monday: 1-2-1 sessions and garden party at the new office Tuesday: Gala Dinner with Hungarian wine and cheese tasting in the old monastery building of the Museum Kiscell. Wednesday: Informal chat and nibbles in the Szimpla Kert.
Markush Forum
Monday May 21st afternoon, preceding the UGM. The Markush Forum provides an opportunity for content users to be updated and shape the further development of ChemAxon’s Markush search and enumeration tools for IP and research.
Thursday May 24th, the UGM will be followed by a dedicated Training day with two parallel tracks: for developers and 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 May 24th, the UGM will be followed by a dedicated Training day with two parallel tracks: for developers and for end users. 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.
Before our Garden party at the office we have a 1-2-1 session where our users can meet with ChemAxon staff to discuss scientific, technical or business issues. Each major product group will have a discussion area where ChemAxon experts will be on call.
For more details on the topics of the 1-2-1 session please check back later.
ChemAxon technology isn't just available from ChemAxon. On Tuesday May 22nd we hold a Partners' lightning round session highlighting how our technologies compliment the products and services of our Partners.
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 $500 for corporate attendees and $250 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.
We look forward to welcoming you in May.
Accommodation
The Hotel Novotel Centrum Budapest will host our UGM in Budapest. Note that the hotel tends to fill quickly so reserve accommodation early. Book your room online now by visiting this page.
Note that besides the ChemAxon conference rate you will find cheaper offers too from the Novotel. The reason is that our conference price includes breakfast and cancellation fee (you can cancel your booking 10 days prior arrival), while the other prices do not. You can decide not to have these options included into your room reservation, and book your accommodation on your own.
ChemAxon moved offices just a few months ago, but this cannot break the tradition of our usual garden party. Following the One-To-One Session we’d like to welcome all of our attendees to a garden party with dinner at our offices.
If you do not want to participate on the One-To-One Session or you just arrive later, there will be a second bus from the hotel to our offices at 6.10 pm. If you choose this option please gather in the lobby of the hotel.
Where? – On the first floor of the event hotel, in the so called Zsolnay Room. For poster and partner exhibitors: You can start setting up your posters or exhibition area from 8.00 am.
The keynote speech of the European User Group Meeting is actually a rather informal talk between our CEO, Alex Drijver and Kent Stewart, Abbott. The speakers in this opening presentation discuss the largest trends in the cheminformatics industry, some more specific topics regarding the changes at Abbott and about ChemAxon’s role in the future’s chemical and biological information technology developments. Kent will give a short overview about how Abbott uses ChemAxon tools – especially our Markush tools.
The JChem family of products have proven their usefulness, flexibility and quality over the years. They provide a stable chemistry base for many applications and services created by customers or third party software providers around the world. We will highlight the main components of the JChem platform (Oracle Cartridge, Instant JChem, Registration Services, Java and .NET API-s, Excel and SharePoint integration, etc.). It will also be shown how it can integrate with old and new products of ChemAxon as well as other software components.
The most important new developments will be mentioned; alongside with a selected set of older, less often referenced functionality, for example reaction and polymer handling.
SureChem provides a short review of the implementation of ChemAxon’s Structure Checker and Standardizer in their patent chemistry data generation pipeline. SureChem uses a fully automated system to extract chemical structures from patent text and images. Generating reliable data requires a robust structure filtration and normalization process. A brief description of SureChem’s ‘best practices’ ” is provided, along with a critique of the current state of technology.
ISIS software has been used for years within the Novartis Institutes for BioMedical Research (NIBR) to draw structures, manage personal substance and reaction collections, and access shared databases. Last year NIBR IT decided to start a project to move to a more modern platform. New tools were evaluated and chosen to replace ISIS/Draw, ISIS/Suite and ISIS/Host. Scientists participated actively in shaping the new solutions.
We have decided to use a combination of tools, including the JChem Cartridge for chemistry databases and Instant JChem as a tool for managing local databases and as interface to shared databases. Here we describe the decision and migration processes and discuss some of the work we have done with Instant JChem, including using it to query our data warehouse and chemical catalogs.
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
JChem for Excel and Instant JChem are both powerful database management tools and various ChemAxon products, including virtual library creation from reactions (Reactor), are seamlessly integrated. In this presentation, we would demonstrate functions and useful tricks: to enable: Structure creation and manipulation in JChem for Excel. Additional visualization tricks with existing Excel functions: Reaction enumeration with Reactor: Chemistry database management in Instant JChem, including different gadgets in Form View, Markush library search, enumeration and visualization.
The presentation will give an overview of the implementation of SciQuest Enterprise Reagent Manager (ERM) and outline how the ChemAxon data cartridge has enabled researchers in the College more fully utilize core functionality within ERM. The focus will be on the both the technical and the process related challenges faced by the project team when implementing the system.
Following the Detroit terrorist incident there was a pressing need for universities to change a number of business processes to strengthen the management and control of hazardous products and materials as highlighted in recent visits to College by the police authorities. The police authorities have identified the laboratory supply chain (i.e. identification, acquisition, use and disposal of chemicals) as one area of major risk for higher education institutions in the UK.
The Head of the Chemistry department subsequently reported that whilst our current e-procurement system can identify what hazardous products have been purchased, when and by whom there is not a robust College-wide management system in place to track and control those products from the point of delivery onwards. This represents both operational and reputational risks to College given that we spend £15m per annum on a complex range of laboratory products and materials of which £1.5m is chemicals related. The Head of Chemistry and Head of Purchasing subsequently investigated and identified a chemical tracking system that would allow the College to manage the complete end to end process – SciQuest’s Spend Director catalogue and Enterprise Reagent Manager. Both Proctor & Gamble and Novartis use ERM although the only other university in the UK that uses the system is the University of Edinburgh and only within the department of Chemistry. While the fundamentals of tracking chemicals is the same there are significantly different business needs and business drivers between pharmaceutical companies and higher education institutions and this in turn impacts how the system will be used and how buy-in from the business community will be gained.
The project was then initiated to implement both elements of the SciQuest system. The first phase implemented the Spend Director catalogue within our Oracle e-Procurement system which went live in March 2011 and is now used across the College to procure chemicals from three of the largest chemical suppliers. The second stage of the project focuses on the implementation of the ERM module which will be trialed initially within the department of Chemistry. The intended go-live of the implementation is scheduled for the 1st May 2012 and therefore, it the full picture in terms of benefits and challenges may not be realized until the end of the six month trial.
This second phase of the project was considerably more complex as it involved both a cultural and process change. While the department of Chemistry were strong supporters of the project and have resources in place to absorb the impact the system would have on day to day activities within the lab, others were more reticent to adopt a system that required a tangible administrative burden.
The following elements of the integration will be discussed in turn during the presentation along with the challenges faced by the project team: – Interfaces with other College systems – ERM to I-Procurement and I-Procurement to ERM – Structure searching tools – Creating materials and searching by structure – Supporting integrated but independent products.
Finally, the presentation will outline the challenges faced by the project team and how risks and issues were addressed. If known, at the time of presenting, an outline of how more effectively researchers could use ChemAxon products in conjunction with ERM to maximize efficiency and to streamline the management of their chemical inventory.
At ChemAxon’s last UGM in the US in September 2011 we presented work in progress on a novel registration service. In this presentation we will update on the development of this service including our experiences in going live and into full operation across our organization.
Microsoft SharePoint is a widely used web-based collaboration platform, which enhances internal communication opportunities between working teams at different locations. ChemAxon’s extensions in JChem for SharePoint provide structure editing, search and filtering in lists, wikis, blogs and discussion boards making SharePoint more attractive for pharma companies. In this talk we will present a drug discovery story to highlight the features of JChem for SharePoint, which may be beneficial in daily routine in the pharma environment.
SharePoint is changing the way we store and search documents at Evotec. With the roll out of JChem for SharePoint and JChem Search for SharePoint we aim to enhance the document search and management capabilities to allow us to work with structural data within the SharePoint framework. This talk will discuss our installation, configuration and the first few months of its operation. We will conclude with some thoughts on the opportunities that it will provide in the future, including providing a platform for chemistry collaboration with our clients.
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
You can meet our partners at their table-exhibits in the lobby of the meeting room any time during the UGM. But the first session of the afternoon will be dedicated to our partners in the main program too.
Our partners will give a brief overview of how they implemented ChemAxon tools and how they extend our solutions. For the exact list of presenters please come back later.
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
ChemAxon’s Instant JChem (IJC) desktop application has been under going a highly intensive development phase recently. On the commercial side it seems to be a clear choice with rapid industry uptake and increased deployment across small companies, academic users and more prominently the world’s major pharmaceutical companies. The repertoire of visualization widgets has increased along with a general improvement in the form building user interface along with core database functionality. Performance and usability enhancements and in particular connection times and query performance improvements are discussed. The scripting functionality available allows for ease of extensibility of the platform. IJC is now more integrated with other applications both within the ChemAxon product suite and with other products, such as Tibco’s ‘Spotfire’. Improved documentation for user, admin and developer has also helped to improve understanding of the product to it’s user base.
This presentation will cover a case-story on strategic choices, design and implementation of a database, using Instant JChem as a key tool for the organization, and management of the discovery process in a biopharmaceutical startup. Having no internal expertise on programming and database set-up, the process has been very much dependent on interaction with ChemAxon support and consultants.
The deployment of Instant JChem to a global R&D community has recently been implemented. The role of an expert user community, both in the testing and roll-out phases of the project, will be highlighted. This will include the management of user requirements and expectations at several R&D sites and the subsequent IJC experience for scientists at different locations around the globe.
Instant JChem (IJC) is an extensible platform for building database based applications for chemistry. The addition of scripting has made extending Instant JChem much easier and more accessible and allows custom functionality to be added on top of the underlying power provided by the IJC platform, such as the form builder, visualization features and the IJC, Marvin and JChem APIs. It might be that your next application could be an IJC application. We will show examples from customers and from the Thomson Reuters DWPI and Markush data.
After the last presentation of the day you’ll be program-free for a while. If you want to participate on our traditional Gala Dinner please gather in the lobby of the conference hotel at 6.00 pm. Buses will leave to the venue.
The evening of the first user group meeting hosts our traditional Gala Dinner. With this event we want to bring you closer to a city that is less known in the world, to Budapest. Every year we try to find a venue which makes networking easier because of the informal environment and program, and in the same time it shows different, interesting – almost unusual parts of our capital city.
This year we’ll have our dinner in the old, monastic building of the Museum Kiscell. Today a museum, once a monastery of the Trinitarian Order, Museum Kiscell will definitely be a perfect scene for our dinner. The evening will start with tasting of Hungarian wines in the cellar of the monastery – if you do not really fancy wine, don’t worry. Following the dinner you’ll have the opportunity to look around the exhibition of the museum.
MarvinSketch and View Java Applets are established technologies for advanced chemical structure drawing and viewing on Web pages. The evolution of web technologies, the fall of Java on the client and the needs of ChemAxon’s users to go to new environments and devices has necessitated a re-imagining of Marvin. In this presentation we describe the main drivers in the work, key decisions and what they will mean for our clients and users, the roadmap; past and future will be discussed and our initial JavaScript Marvin GUI development demonstrated.
We have developed a chemical structure based chemical ontology that allows to automatically annotate compounds with their chemical classes in databases or text documents. Thus, one may now retrieve compounds that are e.g. steroids, without the need to know the different substructures of compounds in the steroid class. In connection with pharmacological effects ontologies it is also possible to query structure-activity relationships or other properties from large document collections. The chemical ontology has been built using a new, dedicated chemical ontology editor SODIAC, which is tightly integrated with ChemAxon’s software tools and has been released in 2012.
ChemAxon’s Naming Technology supports IUPAC and common name to structure conversion, and vice versa. It also recognizes CAS Registry number. Various improvements have been made recently to dramatically increase its precision and coverage. Powered by the Naming Technology, Document to Structure (D2S) is able to extract chemical information from documents with location data. The latest version applies text OCR technology and can even work on scanned PDF documents. Based on the Naming technology and D2S, a free online service, chemicalize.org, has been set up. All chemical information in the text is extracted and the uploaded document can be visualized in Document Viewer with structures interactively displayed. Furthermore, all structures are indexed and can be found through structure and keyword search on the site. In this presentation, we would like to demonstrate the usage of Naming, D2S and chemicalize.org. Post-processing, including structure correction with Structure Checker, streamlining the workflow with KNIME, is also discussed
We present a grid-based solution for chemical named entity recognition (NER) in full text patent collections that are provided in native PDF format. Our architecture identifies and extracts IUPAC and trivial names of chemical compounds and translates them into InChI keys that can subsequently be used to generate structures for each identified entity with Marvin. All structures are finally stamped into the original PDF as ‘pop-up’ chemicals together with hyperlinks to corresponding sites of ChemSpider and Pubmed. A generated bookmark tree inside the PDF allows convenient access for all identified compounds. Additionally all retrieved chemicals are stored in a ChemAxon Instant JChem database together with a reference to the original patent. Instant JChem enables structural search for the processed patent collection and various filtering options. The work-flow is based on UIMA (Unstructured Information Management Architecture) and can easily be adapted to incorporate different chemical NER tools. UNICORE is used to access grid resources for efficient parallelization of all processes.
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
Evaluation of chemicalize.org indicates it not only complements and benchmarks commercial patent databases but also for academic groups interested in interrogating only small sections of the medicinal chemistry IP landscape, may provide an alternative. It has powerful flexibility when combined with other open tools and sources to identify not only novel drug discovery compounds but also link them to SAR. For example, patent office metadata queries, keyword searches in freepatentsonline (FPO) or EBI CiteExplore patent abstracts give useful drug target recall via gene names and simple Boolean conditions (e.g. DPPIV OR dipeptidyl peptidase AND inhibitor). Identified patent texts can then be chemicalized in seconds from any espacenet or FPO URL and quickly eyeballed for drug-like exemplars. Additional IUPAC conversions in problematic cases can be accomplished by re-inputting text from Notepad and iterating OCR fixes such as I>1. For recalcitrant cases the OPSIN tool (http://opsin.ch.cam.ac.uk/) will sometimes succeed or highlight the error point. Relevant exemplar listings, separated from common reagents, can be surfaced in a convenient form (e.g. https://sites.google.com/site/cdsouthantest/home/us7687625) to allow SDF download from chemicalize followed by uploading to PubChem. In this case, a DPPIV filing by Takeda, 68 of the 99 structures had exact matches. By aggregating the PubChem patent chemistry sources of Thomson Pharma, IBM and EPO at just over 5 million CIDs we can intersect these with 48 of the 68 from US7687625 by exact match. We can also intersect with ~ 0.7 million ChEMBL journal curated compounds, in this case identifying CID 11153488 as an aloglyptin analogue published by Takeda. Linking IC50 or Ki SAR results requires inspection of data tables in the PDFs and matching the more potent values to the examples converted by chemicalize. The individual SMILES can also be used to find PubChem exact matches or similarity clusters. The self-archiving feature of chemicalize has useful circularity for similarity detection as more patents and papers get extracted by more users. In combination with PubChem 2D or 3D clustering this allows “walking” between patent series. Not only can Chemical similarity alerts can be set via MyNCBI and patent searching alerts at FPO but also (http://scibite.com/) provides automated gene name-to-patent matches from EPO to Twitter. Thus, newly published patents with good IUPACs in any full-text source can be chemicalized, checked against PubChem in minutes and, on a good day, be linked to SAR data. By definition new structures should be PubChem-ve (i.e. novel). Some may eventually enter PubChem via commercial source feeds, but they can be archived locally using JChem for Excel for similarity checking against any source. Chemicalize also proved useful for extracting structures from abstracts and full-text articles. An example for the former was a recent Takeda DPPIV abstract (PMID:21764322) from which the lead structure was chemicalized, matched to CID 10271081, the PDB structure and a Takeda patent via the ChemSpider-to-SureChem link. An open full-text PubMed Central review on DDPIV inhibitors (PMID: 21847463) provided context to this area and chemicalize recognized structures for four approved glyptin anti-diabetic drugs.
The value of patents is that they contain information often not available anywhere else, and are a window into what a company is thinking about doing. However, that information, and the opportunities they may reveal, is often hidden deep within patents and the Markush structures they disclose. This talk will focus on how that information is described in patents, and how it is translated by analysts into Markush data available through Instant JChem so that it can be retrieved and analyzed.
Markush structures are widely used in combinatorial libraries and chemical patents. However, the flexibility and complexity of Markush structures make them difficult to create, index, visualize, search, and enumerate. Recent improvement of ChemAxon’s applications makes Markush structure handling easier and more efficient. This presentation will give an overview of ChemAxon’s latest Markush technology, including various Markush variations supported, Markush navigation, enumeration and creation. Now our technology also has the capability to search the full Thomson Reuters database, including Markush and exemplified structures, and other data, via Amazon Cloud. Recent development added new features, such as adding notation, batch search of multiple queries, retrieving patent documents, etc. All these features are seamlessly integrated with the latest Markush search interface.
The integration of internal and external chemical information is a vital and complex activity for the pharmaceutical industry. First, finding non redundant data sources with comprehensive data sets and available chemical formats for merging internal and external chemistry data collections is a difficult activity. Assessing the yield of text mining approaches and the quality of human annotation is important in determining whether externally derived data sets are comprehensive or adequate to permit decision making on novelty, infringement, or patentability issues. The cost of procuring data, redundancy of information, and the labour costs of deriving accurate data sets are additional issues. That is the case of exemplified molecules; managing the integration and matching of Markush definitions represent more complex data resolution problems. The development of use cases act as a guide to prioritize the types of integrations that may be required, promotes methods to achieve these integrations, and identifies the level of confidence that can be expected from such operations to determine whether decision making can be based on assurance that the assumptions are correct. It is also important to develop cross disciplinary teams to develop use cases across a range of discovery chemists, informatics and patent practitioners, as their combined requirements are important to maximize the use of information and their individual usage or data handling skills and knowledge are vastly different. The cross disciplinary teams are capable of extending the variety of use cases, as well as extracting the meta knowledge of data sources and perspectives for using chemical information, and also allows ownership to be distributed between silos in the organization. This talk will describe certain use cases, methods by which they can be achieved, and the underlying data issues that make them operate to enable comparisons between internal chemical understanding and trends identified from external data collections.
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
Following the lunch you can join the poster presenters in the meeting room’s lobby for a walkthrough of the exhibited scientific posters. For the exact list of posters please come back later.
Whilst ChemAxon has always provided professional services, this is now being put on more formal footing with the set up of a professional services group within ChemAxon. This ranges from building custom applications to providing on-site support for migrating to the ChemAxon platform. We will provide examples, and describe the plans and tools as we increase our capabilities and capacity in this area.
In a collaboration with ChemAxon we have developed a web-based interface for searching and browsing chemical reaction data. The system was designed to accommodate data from both an historical ISIS/Base database as well as our current ELN. We focused on ease of use, maintainability, and flexibility.
In this talk we’ll discuss the design and implementation process and, conditions permitting, demo the new software.
IDBS has called upon the ChemAxon Reactor toolkits to assist in building a solution for chemists running parallel synthesis experiments. The solution supports enumeration of reactions and products plus entry of associated stoichiometry parameters. It is available as part of IDBS’s E-WorkBook ChemBook product so that scientists can enumerate reaction products and capture all of the context and management and sign-off information associated with the experiment in a single application. This talk will cover some of the technical design and implementation challenges faced building this solution and how they were overcome. The talk will feature reflections on the solution now in production and assisting the scientific workflow, from the perspective of an IDBS and now indirectly, a ChemAxon customer.
A radical restructuration of our ChemAxon-powered virtual screening web server is ongoing: adoption of new standardization rules, inclusion of various ISIDA property-labeled (thus implicitly pH-sensitive) descriptors, parallelization of time-consuming tasks on a Torque queuing system-based cluster, and Kohonen-map driven acceleration of similarity-based virtual screening. By the date of the UGM, we expect the entire ZINC set to be pH-dependently standardized (including tautomerization), described and uploaded into ScreenDB. Virtual Screening benchmarks will be performed and reported – or not! If the planned uploading fails, the discussion will (unfortunately) focus on the encountered problems…
In the breaks of the UGM you will have the opportunity to read through the scientific posters exhibited, and to have a chat with ChemAxon partners about their solutions. Our partners will have a small exhibition area in the lobby of the meeting room where the break menu will be served too. This way you can catch some interesting topics among two bites.
We recently introduced Drug Profile Matching (DPM), a novel affinity fingerprinting method capable of predicting the complete effect profiles of small molecules based on their interaction patterns which are generated by flexible docking to a series of rigidly handled non-target protein active sites. DPM was found to classify molecules excellently and the question naturally came up: What is the contribution of 2D and 3D structural features of the small molecules to the surprisingly high prediction power of the docking-based DPM? To answer this question, the performance of DPM and 2D and 3D similarity fingerprinting approaches using ChemAxon JChem Base and Calculator Plugins were compared. Drug classification was carried out for a two-level hierarchical effect database using a set of cca. 1200 FDA-approved small molecule drugs. To get a more realistic view about the feasibility domain of DPM, its predictive power was also tested on external data. We found that 2D and 3D similarity fingerprinting of rigid structural categories produced as similar high prediction power as DPM, however, for many effects DPM was able to overcome the common screening problems of 2D and 3D similarity searches arising from the presence of structurally diverse molecules.
2D fingerprint-based similarity search is certainly the fastest and most robust ligand-based approach to select focused libraries from multi-million compound repositories based on the structure of known biologically active compounds. Even though the hit rate often reaches 2-5% further improvement is required. One of the standard methods is to filter the similarity search results according to the calculated physico-chemical parameter space of the known active agents. Another ligand-based approach is to determine the shape/flexibility similarities of the 2D search results towards the known actives and such values can be used for ranking and filtering the 2D similarity results. This novel tool, Screen3D, allows fully flexible matching and can also align flexible database compounds to rigid query molecules using on-the-fly generated conformation ensembles.
Two types of 3D similarity screening methods are available in Screen3D: “Shape” and “Match”. While “Shape” evaluates full molecular shape similarity measures that can model ligand binding to a protein’s active site, “Match” intends to explore key atoms in ligand binding while the actual shape of the molecule is not considered.
In our studies we applied the „Match” function analyzing a previous phosphodiesterase 5 (PDE5) 2D similarity search and screening campaign in order to identify 3D similarity threshold. For 2D similarity search using Instant JChem we set the similarity threshold to 0.65 Tanimoto coefficient. For the first screening round we identified 0.35 cut-off values for Screen3D while for the second round screening using close analogs 0.5 was determined (while 2D similarity values where over 0.8 Tanimoto). In order to validate our results we applied the 0.35 values for refinement of a completely new 2D similarity search generating PDE4 focused libraries.
In our presentation the PDE5 analysis, the selection of the PDE4 focused library and its biological evaluation will be presented.
The fast prediction of NMR spectra is of great importance in structure elucidation and validation of molecules. ChemAxon’s NMR Predictor is able to predict 13C and 1H NMR spectra for standard organic molecules containing the most frequent atoms (H, C, N, O, F, Cl, Br, I, P, S, Si). The demonstration will summarize the physicochemical models behind the prediction of spectral parameters (chemical shifts and coupling constants), the accuracy of the predicted results, the features of the NMR graphical user interface and the other ways of predicting NMR spectra (cxcalc and NMR API). The second part of the presentation will focus on ChemAxon’s solubility predictor, currently under development, looking at the features of logS prediction with a special emphasis on the prediction of intrinsic and pH dependent solubilities.
Over the years, Evotec has built up a library of custom calculators. With the new Services interface built in to Marvin, we are now easily able to integrate these across our own applications as well as ChemAxon’s. With their additional development into KNIME nodes, we have made a good step to “write once, deploy everywhere” for our calculators and have enhanced what the chemists can do for themselves on their desktops (without the need to ask for help!). This talk will go through the development process for integration our calculator algorithms into Marvin and KNIME and how our scientists are using them to enhance their project work. We will also (try and) give a live demo of building and deploying a new calculator into Marvin and KNIME – if the services are working in Instant JChem, we will also show that.
Following the closing words of the UGM you will have time to refresh yourself before our informal dinner. If you want to join us, please gather in the lobby of the conference hotel at 6.10 pm.
We’ll have our final social event in the Szimpla Kert which shook up Budapest’s nightlife about 10 years ago. Some university students decided to create a pub which is home for some 21st century art too. The interior design of the Szimpla Kert is rather unusual, though definitely interesting. This pub was the first to be opened in its genre and getting more and more popular.
If the weather allows, we’ll have a rather informal dinner and chat on the courtyard of the pub.
Throughout the day we host two tracks of training. Please visit the trainings’ page for more information: agenda of the Developers’ Training and of the Application Focus Training. We’ll use the conference hotel’s rooms for all the training tracks.
Where? – On the first floor of the event hotel, in the so called Zsolnay Room.
Markush Forum
May 21st, informal lunch at 12:30 pm in the restaurant of the event hotel, session between 1:00 pm - 5:00 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.
Information Managers, Patent information Specialists, Research Managers concerned with investigation of patent space, Patent Attorneys, Business Intelligence Analysts.
May 24th, approximately between 9:00 am - 5:30 pm in the event hotel. 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. 8:50 am - 12:30 pm - Introduction into ChemAxon's Marvin Suite
8:50 am - Opening Remarks - Miklós Vargyas
9:00 am - Structure representation, structure i/o, building molecules - János Kendi
10:00 am - Introduction to Marvin - István Fajth, Tamás Vertse
11:00 am - REFRESHMENT BREAK
11:30 am - Calculator plugin integration - Zsolt Mohácsi
12:00 pm - Custom Structure Checker implementation - István Rábel
12:30 pm - LUNCH
Afternoon session
appr. 1:30 pm - 5:30 pm - Introduction into ChemAxon's JChem Suite
1:30 pm - Chemical database concepts, an introduction to JChem Base - Adrián Kalászi, Tamás Csizmazia
2:30 pm - REFRESHMENT BREAK
2:45 pm - Chemical database programming, examples of JChem Base API - Nóra Máté, Péter Kovács, Róbert Wagner
3:45 pm - REFRESHMENT BREAK
4:00 pm - Instant JChem - Tim Dudgeon, Petr Hammernik, Erin Bolstad
5:30 PM - Closing remarks
101 FAQ's to be answered:
Structure Representation:
How to build molecule from API?
How are molecules with R-groups, S-groups represented?
How to read and write features and molecules in various file formats (SDF, Marvin document file, CxSmiles...)?
What are the components of a reaction?
Marvin Applets and Marvin Beans:
Marvin Applets and Beans - what is under the hood?
How MarvinView and MarvinSketch can be embedded in an HTML page?
How to communicate with Marvin Applets from Javascript?
How to fine tune the applet, to achieve the best available performance?
How to embed Marvin in Swing based Java applications?
How Marvin can be customized in client applications: how to customize the GUI, how to customize structure display, how to customize the editing?
How does image import and export work in Marvin, which facilities can be used to create export options based on GUI or based on predefined display settings?
How to customize templates and abbreviated groups in Marvin?
How to change the structure while transferring between the viewer and editor?
What tools does the Marvin library provide for other specific tasks?
Where and how to find valuable information about the various settings and the wide range of tools can be used from Marvin Beans library?
Calculation Integration:
How external calculations can be integrated into ChemAxon products?
How to implement a simple calculation in Java, and use it in MarvinSketch, cxcalc, and IJC?
How to access web services from MarvinSketch, cxcalc, and IJC?
Structure Checker:
How to implement new checkers and fixers for Structure Checker?
How custom checkers and fixers can be integrated into ChemAxon applications?
JChem:
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 handle tautomers?
How to standardize structures during compound registration and in hit visualization?
Instant JChem:
How does the API relate to IJC’s two layers of functionality (DDL and DML)?
How does one add a new entity or field via scripting?
How does one import and export files, and add fields/properties to exported files?
What data manipulation can be done via SQL, and what must be done via IJC in order to keep registries intact?
How do you implement other tools from the script level (eg Standardizer)?
Application focus training
May 24th, approximately 9:00 am - 5:30 pm in the event hotel. 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. The session starts at 9.00 am but we will be helping attendees set up their machines from 8 am.
Introduction to ChemAxon technologies with Marvin and JChem for Excel hands on training
The first presentation of 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. After the general introduction of our product line we'll have two parallel hands-on training tracks on Marvin Suite and on JChem for Excel.
9:00 am - 10:30 am
ChemAxon technology
This lecture explains the usage of ChemAxon’s core technology. The lecture will discuss the chemical structure handling and basic technology from an end uses point of view. The lecture will also explain the various product categories and dependencies.
10:45 am - 12:00 pm
Marvin hands on training
Basic, advanced features and latest improvements of Marvin are covered.
10:45 am - 12:00 pm
JChem for Excel hands on training
The hands on session will provide working exaples for basic and advanced usage of JChem for Excel capabilities.
Advanced usage of ChemAxon technology
This workshop session is designed to continue 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.
1:00 pm - 2:30 pm
Instant JChem hands on
Topics such as database management, hierarchical tables, form view design, standardization, structure searching, Markush structure searching, Groovy scripting are covered.
Reaction enumeration by Reactor will also be discussed.
2:45 pm - 4:00 pm
Pipelining ChemAxon hands on
This session covers the use of ChemAxon technology in Pipeline Pilot and Knime. Database management, property calculation, structure searching, similarity searching, enumeration (Markush enumeration and reaction enumeration) are covered.
