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AKos GmbH Newsletter June 2011

AKos Consulting & Solutions Deutschland GmbH
+49 7627 970068
+49 7627 970067
Fax to Mail
+49 1805 744743 8318
General Information:


Who benefits: Content:
Every chemist and biologist CWM Global Search - new features
Electronic Lab Notebook - affordable for everyone

Accelrys acquired Contur Software AB
Medicinal Chemist Predicting Potential Adverse Drug Reactions
Proteax - spreadsheet for proteins
Modelers free Discovery Studio Visualizer
IT Managers Decrease IT expenditures
Webinar schedule for
Pipeline Pilot from Accelrys
All Accelrys European User Group Meeting, Oct 11-13, Athens

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Please forward this to a friend, who might be interested.

CWM Global Search allows searching the Internet by structure, synonym and CAS Registry Number. In a Quick Search, we return structure, names and CAS Registry Numbers* within seconds. The Global Search allows a comprehensive search and the resulting links are organized by topics. A search by name can automatically invoke another search by structure and/or CAS Registry Number, or any combination of these. CWM Global Search presently searches 50 free chemical and pharma relevant databases  -- containing more than 100 million pages which associate chemical structures with data.

All you have to do is to open the URL http://cwmglobalsearch.com/gsweb in your Internet Explorer or Firefox on Windows, or Safari on Macintosh.


Please let us know of sources of your interest and we will try to include them.

Name to Structure
Type a valid systematic chemical name in the associated textbox. A click on the 'Name to Structure' button tries to convert the chemical name to a structure. If the conversion was successful, the structure box of the QuickSearch page will be updated with the generated structure.

Chemical Name Search
We explained the last time how to use this option for substructure search by name. This option also helps if you have an IUPC name that has an error. Leave away the brackets search by fragments and the system suggest structures that match the fragments in the name.

New features:

  • Quick Search starts automatically if user press ENTER key after entering name or CAS Registry Number query
  • Pressing ENTER key after entering/editing Names/CAS Registry Numbers in GS query page, automatically populates name/CAS Registry Number listbox
  • Visible indication of used ‘Predefined profiles’
  • Possibility to Save/Load QuickSearch and Global Search queries
  • New datasource: EBI search
  • If more than one query term is entered in the text search field we create automatically two queries, one with quotation mark, and one without. This reminds the user if he wants to search by "or" or by "and" logic.
  • The Quick Search has two extra options, the "Chemical Name Search", and "Tautomerize structure query".
  • Generation of IUPAC name for chemical structures in the QuickSearch page using ChemAxon's Structure to Name service.
  • Structure boxes are now automatically resized.
  • New added horizontal and vertical splitters makes it easier to use CWM Global Search on devices with small screens.
  • Support for chemical structure searches in Wikipedia.
At the first time you will be asked to install the Microsoft Silverlight Plug-In, provided it is not already installed. 

We recommend to start by reading the installation notes at cwmglobalsearch.com/installation

A free version is available that is restricted to searches at Google, PubChem, ChemSpider and AKosSamples.

The full version is 240 Euro per user per year.

We sincerely are interested in your feed-back. Please use the feedback button in the application. 

Electronic Lab Notebook
affordable for everyone!


iLaaber - the cloud-based ELN

With only a few clicks you can launch a scientific workspace, invite your colleagues and collaborators and gather all your experiments in one secure and searchable location. With iLabber you do not need to hire costly consultants nor purchase any additional hardware. With iLabber you can start your first ELN experiment in five minutes...


Spot the difference - and get it right!
Can you name proteins just by looking at them? Proteax DerNot expressions clearly show you how much two proteins differ. Works with cyclic chains too.

Protein SAR tables - impossible you say ? No, not at all.
Proteax can name your biopharmaceutical candidates so you get consistent and meaningful labels for your protein SAR tables.

Having trouble with your weight ?
Does the analytical department claim a molecule weight of 9243.5 Da but your sequence says 9202 Da ? Let Proteax enable seamless communication between mass-spec and medicinal chemistry.

Can your chemists and bioinformatics people agree ?
Is it a structure ? Is it a sequence ?... Imagine that they used Proteax - a consistent way of representing biopharmaceuticals that lets you see molecules as sequences or structures as you please.

"Can you generate 1000 controlled mutations for me this afternoon ?"
Applied DerNot expressions let you create protein derivatives through simple Excel expressions. With chemically consistent results


Proteax® for Spreadsheets 1.3 released
Proteax for Spreadsheets 1.3 is now ready for download. Improved layout and graphical rendering of chemical structures.

  • The image to the right is an actual rendering of Cyclosporin CsA generated directly from sequence. Unmodified natural amino acids are shown as green "bubbles".
  • Optional name and number residue labels.
  • 64-bit Microsoft Excel® 2010 directly supported.
You can get a fully functional trial version of Proteax for Spreadsheets by downloading it here.


Proteax Desktop and Proteax Cartridge downloads
With the release of Proteax 1.3 all Proteax products will be available for direct download from the Biochemfusion web site.
  • Proteax Desktop - Use Proteax from .NET, Python, Pascal, or C/C++.
  • Proteax Cartridge - Use Proteax SQL extensions and indexing inside Oracle® databases.

Discounted licenses until year-end
There is still time to get a Proteax for Spreadsheets license for only € 350,-. This is an introductory offer that expires December 31st.

Can your chemists and bioinformatics people agree ?
Is it a structure ? Is it a sequence ?... Imagine that they used Proteax - a consistent way of representing biopharmaceuticals that lets you see molecules as sequences or structures as you please.

"Can you generate 1000 controlled mutations for me this afternoon ?"
Applied DerNot expressions let you create protein derivatives through simple Excel expressions. With chemically consistent results

Predicting Potential Adverse Drug Reactions Caused by Off-Targets

Using AurPASS


Free Webinar


When ?



Thursday, June 30th


8:00 AM



11:00 AM



5:00 PM 







Find us on Facebook Follow us on Twitter View our profile on LinkedIn 

Product Development

Aureus Sciences - Make the right decisions with data you can trust 



Adverse drug reactions resulting from off-target activities account for the majority of drug withdrawals from the market. With the credo 'fail early, fail cheap', in silico methods are expected to gain largely in importance with improved models that are able to address different aspects of drug safety at early stages of drug discovery projects. These techniques consist of a spectrum of methods designed to efficiently search large compound databases in silico for molecules likely to have a desired biological activity or to avoid unwanted off-target side effects.  


In this webinar, we will be introducing AurPASS (Aureus Prediction of Activity Spectra of Substances). You will learn how this application exploits high quality experimental Structure-Activity Relationship data combined with PASS probabilistic ligand-based methodology to generate in silico biological activity profiles of new substances and therefore help gain insights into potential off-targets.


Following the presentation, this webinar session includes a demonstration of how AurPASS generates in silico pharmacological profiles and helps investigate potential adverse effects and related safety pharmacology issues.


What Will Be Covered


  • Generation of in silico biological activity profile(s) of your compound(s) on different target families (GPCRs, Kinases, Ion Channels, Nuclear Receptors).  
  • Probability estimates of predicted activities for a better assessment of the activity spectrum.  
  • Detection of potential off-target effects earlier in drug discovery process.


Who Should Attend 


  • Medicinal chemists and pharmacologists
  • Computational chemists
  • Safety pharmacologists

AurPASS® (Aureus Prediction of Activity Spectra of Substances) is a software tool which exploits high quality experimental SAR data to generate in silico biological activity profiles of new substances.

AurPASS® is a ready-to-use software tool running with several SAR bases extracted from the Aureus knowledge bases. These include GPCR, Kinase, Ion Channel, Nuclear Receptor, Protease, and hERG.

AurPASS® is the result of the combination of first-in-class systems and high level expertise provides robust computer-assisted estimates with more than 90% accuracy.

PASS (Prediction of Activity Spectra of Substances) predicts Biological Activity Spectra of compounds.

Biological Activity Spectrum of a compound.
X-Axis = Pa-Pi
Y-Axis = Activities
Pa = probability that the compound has this activity
Pi = probability that the compounds does not have this activity
Only a few of the more than 4000 activities are shown for which PASS is trained.

We are very pleased to announce that the latest release of our free Discovery Studio Visualizer software, version 3.0, is now available for download at: http://accelrys.com/products/discovery-studio/visualization-download.php


With Discovery Studio (DS) Visualizer, the following features are available for free:

  • Visualization:

    •   Advanced, flexible molecular visualization tools

    •   Publication quality molecular images

    •   Hardware acceleration and stereo support

  • Ligand-based design:

    •  Sketching and fragment building tools

    •  Manual pharmacophore generation

  •  Macromolecule design:

    •  View and edit molecular sequences

    •  Superimpose and edit protein structures

  • Web ActiveX Control (New update coming soon!)

    •  Visualize and interact with molecules in Microsoft Office documents and Internet Explorer

New with version 3.0:

  •  Advanced graphics rendering:

    •  On supported graphics cards we can now offer depth cue, depth-blur and shading effects

  •  2D Diagram:

    •  Create 2D ligand-receptor interaction diagrams directly in the free Visualizer.

  •  New Storyboard mode:

    •  Capture key scenes in the Molecule Window and save them to share with colleagues.

  •  Sequence window:

    •   Handle and align sequences with multiple chains (e.g., Antibodies).

    •   In Chain view, you can swap chain order and align independently. 

All this is available for free!  To learn more about the visualization capabilities in DS Visualizer 3.0 download our data sheet: http://accelrys.com/products/datasheets/discovery-studio-visualizer-30.pdf .Download DS Visualizer 3.0 today at: http://accelrys.com/products/discovery-studio/visualization-download.php 

Best regards, Adrian Stevens (Product Marketing Manager, Discovery Studio)

AKos GmbH is the exclusive reseller for Accelrys in the countries East of Austria until the Chinese border and South including Macedonia and Serbia, with the exception of academia in Russia and Poland.

The products of Accelrys are:


Webinars by Accelrys:

Quantifying the Value of Pipeline Pilot, with Axios Partners.
The recording is available if you would like to review it at a time that is convenient http://media.accelrys.com/webinars/pipeline-pilot-85/6-16-11-quantify-value-pp.wmv
You may also be interested in upcoming webinars in this series

  • June 28: Enhancing Data Pipelining with Document Search and Text Analysis

  • July 19: What’s New in Pipeline Pilot 8.5?

 Learn more and register here: http://accelrys.com/events/webinars/pipeline-pilot-8/index.html  


European User Group Meeting
Oct 11-13, Athens


Academic registrants receive a 250 $ discount through the start of the conference, but are encouraged to register today. Learn more by visiting the EUGM website.


* CAS Registry Number® and Synonym CAS Registry Number, SciFinder are registered trademarks of the American Chemical Society (ACS). All Rights Reserved. JDraw is a Java applet structure editor from Accelrys, Inc.