Ex h ib i t ion News le t te r

GCC 2013

www.gdch.de/gcc2013

TOPICS

List of Exhibitors

List of Sponsors

Pre-Conference Workshops

Room Plans

Exhibitor One-Pagers

9th GERMAN CONFERENCE ON

CHEMOINFORMATICS

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 http://www.gdch.de/gcc2013. 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

List of Exhibitors

CEPOS

www.ceposinsilico.com

CERTARA www.certara.com

ChemAxon www.chemaxon.com

Chemical Computing Group

www.chemcomp.com

Dotmatics

www.dotmatics.com

KNIME www.knime.com

OpenEye

www.eyesopen.com

Georg Thieme Verlag www.thieme.de

Xemistry www.xemistry.com

List of Sponsors

Gold Sponsor

Chemical Computing Group

Silver Sponsor

Knime

Bronze Sponsor

Dotmatics

General Sponsors

Chemistry Central

iChemLabs

Thieme

Exhibition & Marketplace Schedule

Sunday, 10th

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 Saal Ulm OpenEye

16:00 – 16:30 Coffee & Exhibition Foyer

Monday, 11th

10:30 – 11:00 Coffee & Exhibition Foyer

15:25 – 16:00 Coffee & Exhibition Foyer

16:00 – 20:00 Poster Session & Exhibition Foyer

Tuesday, 12th

10:30 – 11.00 Coffee & Exhibition Foyer

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.

Exhibition/Poster Session Floor Plan

Contacts: Americas: Email: cepos@cacheresearch.com URL: http://cacheresearch.com Tel: +1 503 830 2772 Europe: Email: info@ceposinsilico.com URL: http://www.ceposinsilico.de/ Tel: +49 9131 9704446

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. EmpireTM-caddle.® is an entirely web-based user interface for Cepos InSilico’s new NDDO-based semiempirical MO program Empire™, which is designed to run in parallel on multi-core desktop computers and on massively parallel supercomputers. EmpireTM-caddle® uses interactive 3D-visialization from Molcad GmbH in standard web browsers. A demonstration version is available at: http://www.cepos-server.com/dev_caddle/caddle/app/login 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 ParaSurfTM 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:

www.hpcadd.com

Will soon include the hpCADD polarizable force field,

so that the force field will be suitable for ParaSurfTM 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: http://sarcaddle.cepos-server.com/ You will benefit from our flexible and customer-friendly distribution solutions.

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.

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.

Customizable fragmentation rules

RECAP fragmentation & R-Group decomposition modules

Fragmentation information is stored with fragments

Generate fragment statistics

Reactor

Reactor allows the user to perform various multi-step virtual syntheses, using generic reaction equations and ChemAxon’s Chemical Terms scripting language.

Pre-built generic reaction library

Fast enumeration

No limitations in reaction type (inter/intra-molecular) reactants and product numbers

No need to preselect reagents

Screen

The Screen suite provides tools for pharmacophore analysis and ligand-based high throughput virtual screening.

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.)

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.

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: +36 1 453 2660

> 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

www.chemcomp.com

dotmatics knowledge solutions . . . www.dotmatics.com

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.

Innovation. Delivered.

Want to know what is coming next?

www.jcheminf.com

CheminformaticsJournal of

Journal of Cheminformatics

Official Publishing Partner and Sponsor of the 9th German Conference on Chemoinformatics

Editors-in-Chief: Christoph Steinbeck (UK) David J. Wild (USA)

• High visibility • Open access• Immediate publication on acceptance• Fast peer review • Online submission

IMPACTFACTOR

3.59

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 report-

ing. KNIME enables the user to visually create

data flows (often referred to as pipelines), se-

lectively execute some or all analysis steps,

and later investigate the results through inter-

active views on data and models.

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 comprehen-

sive range of enterprise products.

Life Science Partners The KNIME core already incorporates hundreds

of nodes for data I/O, preprocessing, cleansing,

modeling, analyzing and data mining and pro-

vides 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 struc-

tures, cell assay images, and other data types

can be visualized to analyse life science data

sets.

Mark your calenders

7th KNIME User Meeting

February 10-11, 2014

Technopark, Zurich

Joining Data Tools and Science

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 dis-

tributed to an SGE computer cluster for parallel execu-

tion. KNIME Team Space Shared repository for KNIME workflows, Metanode

templates and data files.

KNIME.com AG, Technoparkstrasse 1, 8005 Zurich, Switzerland. contact@KNIME.org, http://www.KNIME.org, Tel. +41-44-445-2660, Fax. +41-44-445-2662

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.

OpenEye Scienti� c Software has been developing large scale applications and toolkits for drug design and molecular modeling since 1997. 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.

About OpenEye, Our Philosophy and Product Line

ROCS

EON

FILTER

OMEGA

FRED

QUACPAC

VirtualScreening

FastROCS

Virtual Screening

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.

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 explora-tion. Docking with FRED is useful for lead optimization, in addition to being an e� ective 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.

MolecularModelingToolkits

CheminformaticsToolkits

OEChem

Zap

Cheminformatics

Omega

OEDocking

Shape

Spicoli

Szybki

Quacpac MolProp

OEDepict

GraphSim

Lexichem

Grapheme

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, � ve All the toolkits are written in C++ and have a stable, documented API. Functionality is also ac-cessible via Python, Java and .NET wrappers.

US Headquarters9 Bisbee Court, Suite DSanta Fe, NM 87508USA+1 505 473 7385

Europe40 rue de St Sylvestre/Lot68660 LièpvreFrance+33 389 589 544

East Coast222 3rd St., Suite 3210Cambridge, MA 02142 USA+1 505 473 7385

JapanAIOS Toranomon 9041-6-12, Nishishinbashi Minato-ku, Tokyo105-0003 Japan+81 3 6206 1425

www.eyesopen.com

The Cactvs Cheminformatics Toolkit in the Python Age Wolf-D. Ihlenfeldt, Königstein, Germany

The Cactvs Toolkit and the Interface Language ConundrumCactvs 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,

i bl d k d f lk d b d 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 multi-threaded fashion if desired. It is still the only toolkit which solves all (pretty simple) test problems posted on the Chemistry Toolkit Rosetta Wiki (http://ctr.wikia.com/wiki/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.

Design ComplicationsObjects (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.

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 multi-language approach – the toolkit now interfaces to both languages simultaneously, in a common executable, with bridges between them.

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.

E l Mi i P j t i T l d P thExample Mini Project in Tcl and Python

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:

ACCLDraw09121305382D

7 0 0 0 0 0 0 0 0 0999 V2000 12.4739 -4.9459 0.0000 O 0 6 0 0 0 0 0 0 0 0 0 0 11.2573 -4.8209 0.0000 Fe 0 2 0 0 0 0 0 0 0 0 0 0 7.7906 -5.0375 0.0000 O 0 6 0 0 0 0 0 0 0 0 0 0 5.8531 -4.9459 0.0000 Fe 0 1 0 0 0 0 0 0 0 0 0 0 5.8531 -4.9459 0.0000 Fe 0 1 0 0 0 0 0 0 0 0 0 0 7.7906 -5.0375 0.0000 O 0 6 0 0 0 0 0 0 0 0 0 0 7.7906 -5.0375 0.0000 O 0 6 0 0 0 0 0 0 0 0 0 0

M CHG 7 1 -2 2 2 3 -2 4 3 5 3 6 -2 7 -2 M STY 6 1 GEN 2 DAT 3 GEN 4 DAT 5 MUL 6 MUL M SLB 6 1 1 2 2 3 3 4 4 5 5 6 6 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 $ehgens delete $ehg

} molfile close $fhout

f=Filter('datagroup',{'property':'G_TYPE','value':'datagroup','operator':'='})fhout=Molfile('split sdf' 'w')

M SPL 2 2 1 4 3 M SAL 1 5 4 3 5 6 7 M SDI 1 4 4.7981 -6.0656 4.7981 -3.6156 M SDI 1 4 9.0081 -3.6156 9.0081 -6.0656 M SDT 2 FDAREG_SGROUP F M SDD 2 9.3481 -6.1856 DA ALL 1 5 M SED 2 A M SAL 3 2 2 1 M SDI 3 4 10.6681 -5.7256 10.6681 -3.8456 M SDI 3 4 13.5081 -3.7356 13.5081 -5.7656 M SDT 4 FDAREG_SGROUP F M SDD 4 13.8081 -5.6856 DA ALL 1 5 M SED 4 B M SAL 5 3 3 6 7 M SPA 5 1 3 M SDI 5 4 7.2581 -5.5156 7.2581 -4.2656 M SDI 5 4 8 4481 -4 2656 8 4481 -5 5156

Availability Supporters

fhout=Molfile( split.sdf , w )eh=Molfile.Read('xmol_6.mol')for g in eh.groups(f):

ehg=g.dup()fhout.write(ehg)ehg.delete()

fhout.close()

M SDI 5 4 8.4481 4.2656 8.4481 5.5156 M SMT 5 3 M SAL 6 2 4 5 M SPA 6 1 4 M SDI 6 4 5.3481 -5.4156 5.3481 -4.1656 M SDI 6 4 6.6581 -4.1656 6.6581 -5.4156 M SMT 6 2 M END

FAQ

h h f d f d dV3.418, which includes all functionality displayed in this poster, is already available for public download from http://www.xemistry.com/academic.

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.

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.

Python 2 or 3? 3.3.2. The interface needs new features introduced 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.