GCC Exhibition Newsletter. 9 th GERMAN CONFERENCE ON CHEMOINFORMATICS TOPICS

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1 TOPICS GCC th GERMAN CONFERENCE ON CHEMOINFORMATICS Exhibition Newsletter List of Exhibitors List of Sponsors Pre-Conference Workshops Room Plans Exhibitor One-Pagers

2 Welcome Welcome to the 9. German Conference on Chemoinformatics (GCC2013) Dear GCC2013 participant, this Exhibition Newsletter will inform you about the pre-conference workshops and the conference exhibition. In addition, the newsletter contains a floor plan, a summarized exhibition schedule, detail information about the content and location of the two pre-conference workshops Furthermore, it includes one-pagers of our exhibitors including latest product news. The technical program for the conference can be found on the conference web site as PDF or online version at A link to the corresponding abstracts can also be found on the web site. The GCC2013 can also be followed via Twitter using the tag #gcc2013 See you on Sunday, November 10 in Fulda, Germany. Sincerely Frank Oellien Conference Co-Chair

3 List of Exhibitors CEPOS CERTARA ChemAxon Chemical Computing Group Dotmatics KNIME OpenEye Georg Thieme Verlag Xemistry

4 List of Sponsors Gold Sponsor Chemical Computing Group Silver Sponsor Knime Bronze Sponsor Dotmatics General Sponsors Chemistry Central ichemlabs Thieme

5 Exhibition & Marketplace Schedule Sunday, 10 th 12:00 13:30 Pre-Conference Workshops This year OpenEye and Knime will offer free pre-conference workshops. Getting your Chemistry right with Knime Saal Köln Knime Combining Modelling and Chemoinformatics: How ToolKits put YOU in the Driver s Seat OpenEye Saal Ulm 16:00 16:30 Coffee & Exhibition Foyer Monday, 11 th 10:30 11:00 Coffee & Exhibition Foyer 15:25 16:00 Coffee & Exhibition Foyer 16:00 20:00 Poster Session & Exhibition Foyer Tuesday, 12 th 10: Coffee & Exhibition Foyer

6 Pre-Conference Workshops Two free pre-conference workshops by OpenEye and Knime will be organized on Sunday right before the official conference opening. The directions to the rooms Salon Köln and Salon Ulm are signposted at the Hotel. OpenEye, Free Workshop: Combining Modelling and Chemoinformatics: How ToolKits put YOU in the driver s seat 12:00 13:30, Room: Salon Ulm The OpenEye Toolkits are programming libraries (sometimes also called Software Development Kits SDKs). They enable the user to address problems in Molecular Modelling as well as Chemoinformatics in straight forward programming. In this workshop we will illustrate how simple scripts can help solve tedious tasks and how powerful the combination of toolkits can be to solve challenging scientific problems. We will show (Python) code snippets to help the users follow the examples. Knime, Free Workshop: Getting your Chemistry right with Knime 12:00 13:30, Room: Salon Köln KNIME is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualisation and reporting. The open integration platform provides over 1000 modules (nodes), including those from the KNIME community and its extensive partner network. In this tutorial we will start with a short introduction into KNIME and concentrate on solving common cheminformatics tasks such as reading and writing common file formats, computing properties, and building predictive models. We will use extensions provided by the KNIME community, such as RDKit, Indigo, or CDK, which are freely available. In the second part we will show how the KNIME Enterprise Server can assist research groups in their daily tasks.

7 Exhibition/Poster Session Floor Plan

8 The next generation of modeling! Cepos InSilico is a spin-off of the University of Erlangen-Nürnberg that develops software based on techniques developed in Tim Clark s groups in Erlangen and in Portsmouth, UK. Cepos InSilico provides surface-based modeling techniques, in silico screening, modeling and simulation software designed to give accurate, generally applicable predictions of biological activity, reactivity, ecological impact and ADME and physical properties. Empire TM -caddle. is an entirely web-based user interface for Cepos InSilico s new NDDObased semiempirical MO program Empire, which is designed to run in parallel on multicore desktop computers and on massively parallel supercomputers. Empire TM -caddle uses interactive 3D-visialization from Molcad GmbH in standard web browsers. A demonstration version is available at: The benefits of Empire include: New software architecture oriented towards future hardware generations massively parallel can calculate very large (tested up to 100,000 atoms) molecules on the semiempirical level with ease Empire communicates via binary data with ParaSurf TM to save time and memory Initial Guess and SCF algorithm are improved! This gives more accurate results as the convergence limits are tighter than in comparable single-core programs Empire is the basis for all future developments of hpcadd: Will soon include the hpcadd polarizable force field, so that the force field will be suitable for ParaSurf TM SAR-caddle. is not just another model-building program; it deploys the latest developments in high end QSAR modeling and provides realistic error estimates and an assessment of the reliability of predictions. A demonstration version is available at: You will benefit from our flexible and customer-friendly distribution solutions. Contacts: Americas: cepos@cacheresearch.com URL: Tel: Europe: info@ceposinsilico.com URL: Tel:

9 Visit us at the exhibition! Life Science Molecular Modeling and Simulation Multi-Criteria Drug Design Lead Identification Lead Optimization Predictive Safety Off-Target Prediction Surflex-QMOD : Quantitative Predictions Based On Physically Realistic, Interpretable Models Surflex-QMOD addresses the physical linkage between a model for predicting ligand affinity and molecular binding modes. As a result, you get more than a mathematical model for numerical predictions of binding affinities, you get a physically interpretable model of the protein binding pocket and ligand poses that explain the physical properties responsible for ligand binding. This allows you to make a direct correspondence between the physical process of protein-ligand binding and the act of prediction. With Surflex-QMOD, you can make quantitative predictions of a drug candidate's affinity for its target, assess the confidence of quantitative predictions, quantify the novelty of drug candidate molecules, leverage SAR from one chemotype to make accurate predictions for novel chemotypes, and combine SAR information from multiple chemotypes into a single model. Muse : Identify and Optimize Lead Compounds Muse is a molecular design workflow that accelerates the identification and optimization of lead candidates. Using Muse, CADD scientists and medicinal chemists can identify novel structures, scaffolds, or side-chains that meet m design objectives; explore lead- and scaffold-hopping; invent new R-groups around a fixed scaffold; and generate ideas that meet multiple design criteria. Using Muse, you can design new candidates that mimic the shape and pharmacophore features of your lead structures, elaborate fragments in the context of a protein binding site for fragment based drug design, generate ideas based on multiple design criteria you choose, and integrate your own properties or CADD models (e.g. docking, ADME prediction, etc.). Muse is Intuitive and easy to use for medicinal chemists, casual modelers and expert computational chemists. SYBYL -X: Molecular Data Explorer, QSAR Project Manager, and more! SYBYL-X has everything you need for drug design and other molecular discovery projects, from HTS follow-up through late Lead Optimization. Easily move from identifying potential lead candidates, to lead optimization projects, or to building a homology model for a target of interest. If you need library design, scaffold hopping, structure based design, ligand based design, cheminformatics, or tools to build a protein model, SYBYL-X has it and more. D360 : Bring Your Scientific Data to Life D360 provides life science researchers with a single point of access to retrieve, analyze, and share scientific data. Eliminating time-consuming, error prone, non-productive hours that scientists spend merging and manipulating data from multiple, disparate sources from early discovery through pre-clinical and clinical drug development, D360 provides quick and easy access to data and enables scientists to deal with data across projects, as well as within a given project. Using D360, scientists report that as many as fifty (50) mouse clicks are reduced to just one, and that assembly of a project SAR dataset can be reduced from hours to minutes, allowing them to spend more time at the bench.

10 About ChemAxon ChemAxon makes desktop applications and software toolkits for structure visualization and management, structure based property predictions, virtual synthesis, screening and clustering. Our products work on all major operating systems and can be implemented into larger systems and web environments. ChemAxon's software is used by leading commercial and academic research groups worldwide. We support academic teaching and research via our free academic package. ChemAxon s Discovery Toolit ChemAxon s Discovery Toolkit is a software suite which provides API, command line and (for some capabilities) integration within ChemAxon s desktop applications - Marvin, Instant JChem and JChem for Excel. By making the functionality available from various access points we ensure the relevance for a wide range of users. Marvin & Calculator Plugins Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, reactions and queries. Calculator Plugins are modules of Marvin and JChem cheminformatics platforms. They include a wide range of structure-based prediction tools to explore the physico-chemical properties of chemical compounds (e.g. elemental analysis, pka, logp, polarizability, conformers, etc.). Fragmenter Fragmenter is ChemAxon s solution for creating molecular fragment libraries based on various cleavage rules. Reactor Reactor allows the user to perform various multi-step virtual syntheses, using generic reaction equations and ChemAxon s Chemical Terms scripting language. Screen The Screen suite provides tools for pharmacophore analysis and ligand-based high throughput virtual screening. JKlustor JKlustor is ChemAxon s solution to explorative data mining in combinatorial chemistry and drug design processes, where a large number of chemical compounds need to be analyzed. Customizable fragmentation rules RECAP fragmentation & R-Group decomposition modules Fragmentation information is stored with fragments Generate fragment statistics Pre-built generic reaction library Fast enumeration No limitations in reaction type (inter/intramolecular) reactants and product numbers No need to preselect reagents Flexible Pharmacophore building (fragment & calculation-based solutions) Configurable Molecule Descriptor Generation (optimization through training) Suitable for ligand based approaches Available (batch, API, workflow nodes, etc.) Wide range of clustering methods Flexible search options; Interactive display Efficient Available (batch, API, Web Services,workflow nodes, desktop applications,mcs viewer Applet) You can try and evaluate all of our software for free. chemaxon.com Graphisoft Park, HX Building H-1037 Budapest, Hungary Phone:

11 > Integrated Drug Discovery Software Package > Platform Independent (Windows, Mac OS X, Linux, Unix) > Embedded Programming Language (SVL) > One Package for Computational Chemists & Occasional Users > Collaborative Customer Support

12 Innovation. Delivered. When others were creating thick clients, we were creating web apps. When others were developing web apps, we were in the cloud. When others were moving to the cloud, we were going mobile. Want to know what is coming next? dotmatics knowledge solutions...

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14 Official Publishing Partner and Sponsor of the 9 th German Conference on Chemoinformatics Journal of Cheminformatics IMPACT FACTOR 3.59 Journal of Cheminformatics Editors-in-Chief: Christoph Steinbeck (UK) David J. Wild (USA) High visibility Open access Immediate publication on acceptance Fast peer review Online submission

15 Mark your calenders 7th KNIME User Meeting February 10-11, 2014 Technopark, Zurich Joining Data Tools and Science KNIME, the Konstanz Information Miner is a user-friendly and comprehensive open source data analytics and integration platform. It seamlessly supports the entire data process workflow covering data loading, integration, processing, analysis, visualization and reporting. KNIME enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. The KNIME core already incorporates hundreds of nodes for data I/O, preprocessing, cleansing, modeling, analyzing and data mining and provides a wide range of interactive views, such as scatter plots and parallel coordinates, to name but a few. Chemical structure representation and tools from leading chemoinformatics vendors are also integrated into KNIME and with community contributed chemistry plug-ins, molecular structures, cell assay images, and other data types can be visualized to analyse life science data sets. Life Science Partners Professional Open Source Software KNIME.com AG is an internationally operating company, based in Zurich, Switzerland, with distributors and partners in Europe, USA and Asia. The company provides consulting and training for the KNIME platform plus a comprehensive range of enterprise products. KNIME Enterprise Server Central repository for KNIME Workflows, user rights management, remote and scheduled execution and web service access. Easy access through WebPortal. KNIME Cluster Execution Single nodes or even complete workflows can be distributed to an SGE computer cluster for parallel execution. KNIME Team Space Shared repository for KNIME workflows, Metanode templates and data files. Support Support and Maintenance Subscriptions are available for KNIME Desktop and KNIME Report Designer. Consulting & Development Services Strategic consulting is providing on all aspects of KNIME plus development services covering topics such as node developments or enhancements to KNIME. KNIME.com AG, Technoparkstrasse 1, 8005 Zurich, Switzerland. contact@knime.org, Tel , Fax

16 About OpenEye, Our Philosophy and Product Line OpenEye Scientific Software has been developing large scale applications and toolkits for drug design and molecular modeling since Our software is designed to accurately quantify the shape and electrostatics of molecules, which we strongly believe are the main drivers in molecular interactions. OpenEye s software product line focuses primarily on virtual screening and lead hopping, and as such includes tools for conformer generation, docking, shape comparison, electrostatics, crystallography, visualization and cheminformatics. OpenEye also makes most of its technology available as toolkits - programming libraries suitable for custom development. Virtual Screening OMEGA QUACPAC ROCS Virtual Screening FastROCS EON OpenEye s Virtual Screening applications include the following: FILTER, QUACPAC, OMEGA, ROCS, FastROCS, EON and FRED. Input compounds are prepared by removal of undesirables (FILTER) and application of a variety of charge models (QUACPAC). OMEGA generates high quality 3D conformer ensembles. For ligand-based virtual screening, ROCS and FastROCS search compound libraries for 3D shape (and chemistry) similar molecules. EON is frequently used in conjunction with ROCS hitlists to identify lead-hops with electrostatic similarity to a query. For structure-based virtual screening, FRED is an exhaustive, rigid docking and scoring application. FILTER FRED Lead Optimization OpenEye has developed novel, award-winning products for lead optimization. Our applications include: BROOD, FRED, SZYBKI, SZMAP, and POSIT. Replacement of fragments with BROOD allows for lead-hopping and SAR exploration. Docking with FRED is useful for lead optimization, in addition to being an effective virtual screening tool. SZYBKI optimizes structures, optionally within a protein binding site. SZMAP explores the environment water encounters in a binding site to guide molecular design. POSIT utilizes information from known ligands to make very accurate, low strain pose positions. Shape Omega Spicoli OEDocking Molecular Modeling Toolkits Szybki Zap Quacpac OEChem OEDepict Grapheme Cheminformatics Toolkits Lexichem MolProp GraphSim Toolkits OpenEye toolkits are programming libraries for creating customized applications which utilize OpenEye technology. Central to the portfolio is OEChem TK, OpenEye s programming library for chemistry and cheminformatics, on top of which a number of other toolkits have been built. Among the seven modeling toolkits, five All the toolkits are written in C++ and have a stable, documented API. Functionality is also accessible via Python, Java and.net wrappers. US Headquarters 9 Bisbee Court, Suite D Santa Fe, NM USA East Coast 222 3rd St., Suite 3210 Cambridge, MA USA Europe 40 rue de St Sylvestre/Lot Lièpvre France Japan AIOS Toranomon , Nishishinbashi Minato-ku, Tokyo Japan

17 The Cactvs Cheminformatics Toolkit in the Python Age Wolf-D. Ihlenfeldt, Königstein, Germany The Cactvs Toolkit and the Interface Language Conundrum Cactvs is a general-purpose chemical information processing toolkit with an extensive set of features. It processes structure, reaction, table and network data. It can read and write over a hundred structure, reaction, table and network data formats, talk to many databases, and has extensive support for Internet-based information resources and standards. It also computes a comprehensive suite of structure and reaction property data and does this all in distributed or multithreaded fashion if desired. It is still the only toolkit which solves all (pretty simple) test problems posted on the Chemistry Toolkit Rosetta Wiki ( The toolkit is designed for rapid solution development by scripting. Its original interface language is Tcl - a capable but lesser known and slightly dated language which nevertheless provides multi-threading features and multi-interpreter insulation far beyond what is possible in, for example, Python. Still, Python has definitely become the accepted standard for cheminformatics and bioinformatics data processing. Most competing toolkits have a Python interface, or are even loadable as a module into a generic Python interpreter. For these reasons, providing a Python interface to the Cactvs toolkit has become essential. This has now been implemented. Quite a number of components of the toolkit are itself scripted in Tcl for example encapsulated standard property computation modules. Legacy components need to remain usable whether a module is implemented in Tcl or Python must be irrelevant regardless in which language the application script is written. This leads to a unique multilanguage approach the toolkit now interfaces to both languages simultaneously, in a common executable, with bridges between them. Design Complications Objects (structure, reactions, tables, networks, files, datasets) are shared between interpreters by default. Any change performed in one language environment is automatically mirrored in the other. One primary interpreter and potentially multiple additional Tcl thread interpreters may operate on these objects simultaneously. The active primary interpreter may invoke its counterpart of the other language for specific tasks. It is even possible to have application scripts consisting of a Tcl and a Python part, for example for re-use of in-house procedure libraries. Example Mini i Project in Tcl and Python ACCLDraw D V O Fe O Fe Fe O O M CHG M STY 6 1 GEN 2 DAT 3 GEN 4 DAT 5 MUL 6 MUL M SLB M SPL M SAL M SDI M SDI M SDT 2 FDAREG_SGROUP F M SDD DA ALL 1 5 M SED 2 A M SAL M SDI M SDI M SDT 4 FDAREG_SGROUP F M SDD DA ALL 1 5 M SED 4 B M SAL M SPA M SDI M SDI M SMT 5 3 M SAL M SPA M SDI M SDI M SMT 6 2 M END Does your toolkit of choice have a Molfile Reader or a RREAL RREADER? The task: Process a set of files with multiple nested, overlapping SGroups of various types, with incomplete atom sets, superatoms and badly aligned annotations. Split the files into individual components by datagroup annotation labels and write a multi-record SDF, preserving the proper subset of SGroups, annotations and all other M xxx stuff in the output. In both language variants, this is a simple exercise for the toolkit: filter create datagroup property G_TYPE value datagroup operator = set fhout [molfile open split.sdf w] set eh [molfile read xmol_6.mol ] foreach g [ens groups $eh datagroup] { set ehg [group dup $eh $g] molfile write $fhout $ehg ens delete $ehg } molfile close $fhout f=filter('datagroup',{'property':'g_type','value':'datagroup','operator':'='}) fhout=molfile('split split.sdf sdf','w') eh=molfile.read('xmol_6.mol') for g in eh.groups(f): ehg=g.dup() fhout.write(ehg) ehg.delete() fhout.close() Availability V3.418, which includes all functionality displayed in this poster, is already available for public download from The full functionality of the standard toolkit will be accessible from Python (exception: concurrent multi-interpreter multi-threaded script execution - generally unsupported in Python) after 3/2014. FAQ Python 2 or 3? The interface needs new features introduced d in 3.3. Where do I get this brand-new Python version? No need. The toolkit includes a complete Python installation. It coexists with other packages. Can I load other Python-linked toolkits into this system? Yes, in principle. But remember, its Python3. You cannot load Python2 compiled modules. Is it Open Source? No. It is free software for academia, though. You may freely redistribute anything you develop for it. Scripting and module APIs are public and royalty-free. Supporters We gratefully acknowledge financial support by Vertex Pharmaceuticals for this project. All improvements implemented with their aid shall be available in the free academic releases.