Consulting & Solutions GmbH
a chemoinformatics company



AKos GmbH Newsletter January 2011

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


Who benefits: Content:
Every chemist and biologist CWM Global Search - the underlying web service
Scientist analyzing and working with Proteins New version Proteax 1.3 - protein variants made easy
IT manager AKos GmbH has resources for Oracle programming and for chemoinformatics projects.
Medicinal chemist, modeler, marketing department AKos GmbH signed an agreement with Evolvus Systems for providing the service to generate custom made databases.
Medicinal Chemist AurPASS® (Aureus Prediction of Activity Spectra of Substances)
Medicinal chemist New developments in PASS.
Medicinal chemist MDDR as personal desktop application.
Modelers Webinar schedule for Discovery Studio from Accelrys

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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 in your Internet Explorer or Firefox on Windows, or Safari on Macintosh-->

We are selling the CWM Global Search web service. What is this, and for what would this be good? 

What is it?

We generate for the structure up to 6 identifiers, 2 InChI keys, 2 InChI names, molfile and smiles depending on the resources selected. We send this information and the free text queries to now more than 50 resources on the web. This web service could be configured from us and installed at a customer site. We also would deliver updates if new resources are added. The results are a collection of links.

 What can you do with this?

  • The chemist has an in-house application to search for suppliers. He has access to SCD, ACD and CHEMCATS. If he cannot find a supplier, or only Chinese ones, one can offer him a “button” and he sends his query to the Internet for a complete search. Such a “button” could be built quite easily in Isentris. One can imagine many applications where the user wants to  augment his in-house searches by a more complete search, i.e. for patents, biological activities, spectra, etc.
  •  KNIME has a node to access web services. The user could send a SDFile to the CWM Web Service, and where he find hits he can invoke other web services (there are about 1000 available right now) to display data and not only links.
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

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

The full version is 240 Euro per user.

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

Some of the new sources in CWM Global Search

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



You only know what you have experienced! Our co-workers have a lot of experience.

  • We sell programs and cooperate with people for building applications. One of us has 18 years Oracle programming experience. His development tools for ORACLE enable us to build applications in days instead of months.

  • Some of us have 20 years experience building chemoinformatics applications in low and high throughput screening, and building and merging structure databases.

  • Others co-workers have experience training commercial and in-house programs.


Custom made databases

AKos GmbH works with Evolvus System that offers as service to build custom made databases for chemical and pharmaceutical companies. This can be databases for a few compounds with all available data, or databases for many compounds with customer selected fields. This can be excerpts from patents or a subsets of already collected data to 3.8 million compounds.  

Predict biological activities with data you can trust


Support the decision-making process and accelerate discovery

Predict biological activities and assess off-target risks

Repurpose drugs through new indications

Optimize lead identification through in silico screening

download product sheet

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.

What's new for PASS?



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

The Biological Activity Spectrum (see right column) of a compound is the collection of pharmacological effects, physiological and biochemical mechanisms of action, specific toxicities (mutagenicity, carcinogenicity, teratogenicity, embryotoxicity, etc.) that can be revealed in a compound's interaction with biological systems. The Biological Activity Spectrum describes the intrinsic properties of the compound dependant on its chemical structure.



Are you familiar with workflow programs? Wouldn’t it be a good idea to have a program that reads a file or gets information from a database, filters the structures by certain criteria, predicts PASS parameters, compares these parameters with known experimental results, selects structures by more criteria, does some modeling, i.e. docking and all you have to do is punch a button?
KNIME and Pipeline Pilot are for chemists the best workflow solutions (in my opinion). KNIME is free, and support is offered by the KNIME company. Pipeline Pilot is sold by Accelrys and has many more nodes and functionalities.

1. Vladimir Poroikov’s group is working on a KNIME node. If required, we can develop a Pipeline Pilot node.

2. Since my programmer is a .NET specialist we developed on Microsoft’s Workflow Foundation a workflow CWM Lead Finder. CWM Lead Finder finds biological similar compounds in two different SDFiles that you can sort by structure similarity, PASS accuracy, and toxicity parameters.

3. The company Aureus collects structures, quantitative and qualitative test data. The idea is to build a comprehensive biological profile of compounds using experimental and predicted data, see above. They have built databases in these areas:

    1. AurSCOPE Global Pharmacology Space (GPS)
    2. AurSCOPE GPCR
    3. AurSCOPE Kinase
    4. AurSCOPE Ion Channels
    5. AurSCOPE Nuclear Receptor
    6. AurSCOPE Protease
    7. AurSCOPE ADME/Drug-Drug Interactions
    8. AurSCOPE hERG Channel

It is expected that the profiles will have many missing data. Aureus has developed knowledge bases i.e. AurPASS GPCR Predictor that augment the experimental data. Now, you can see exactly which compounds were used to build the knowledge base in PASS.

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.



Drug Data Report
as desktop application

Drug Data report is one of the most used databases to get structures and biological effects. MDDR is very handy to get SDFiles with compounds of desired activities. We managed to load the MDDR SDFile into Isentris Personal Edition. Isentris Personal Edition is the successor of ISIS/Base. This means you have now a solution to work with MDDR without the need to install a server system. Isentris Personal Edition is strictly a personal system. You cannot install it on a server. MDDR is licensed by Accelrys.  



Discovery Studio



Thursday 13th of January 1:30 PM UK Time                         

Title: An Introduction to Discovery Studio 3.0 – Tien Luu / A. Stevens

Abstract: The release of Accelrys’ Discovery Studio 3.0 in November extends our portfolio of small molecule drug design and market leading biological simulation tools and is focused on bringing new science from Accelrys and our partners, improved performance, and key enhancements to our users. This webinar will introduce users to key enhancements within the client designed to improve usability and encourage collaboration, as well as providing an overview of the new scientific developments.

Thursday  10th  of February  1:30 PM UK Time

Title: Protein Design tools in Discovery Studio 3.0: Computational stability prediction and  Computational Alanine Scanning – Anne Goupil  / A. Stevens

Abstract:  One of the primary goals of protein design is to engineer optimized proteins by introducing mutations.

Protein thermal stability is a key issue for chemical, biotechnology and pharmaceutical industries. We will present a new set of tools available in Discovery Studio 3.0 and  show how to calculate  mutation energies as well as  predict stabilizing mutations

Similarly, Protein-protein interactions are a key components of signal transduction.. Methods for predicting energetically important amino acids (interaction hot spots) at protein-protein interfaces are of increasing interest. We will present a new set of tools available in Discovery Studio 3.0 and show how to predict computationally derived interaction hot spots.

Computational results will be compared to experimental data on a set of selected examples.

Thursday  24th  of February  1:30 PM UK Time

Title: Automatic Creation and Validation of Pharmacophores derived from Receptor-Ligand Complexes Tien Luu / A. Stevens

Abstract: A pharmacophore is a model which represents the key physico-chemical interactions, between a receptor target and ligand, that mediate biological activity. In DS 3.0 users can automatically create a series of pharmacophore models representing a receptor-ligand complex, and have these validated with known active and inactive compounds to determine the best pharmacophore for hit/lead identification.

Thursday  10th of March   1:30 PM UK Time

Title: Discovery Studio 3.00 /Pipeline Pilot 8.00 Integration - Anne Goupil  / A. Stevens

Abstract:  Discovery Studio is build on Pipeline Pilot™ platform technology,  it is therefore possible for scientists to access any computational codes available in Discovery Studio at the Pipeline Pilot level. We will show through examples how scientists can customize or build their own protocols to automate tasks and or meet their precise needs.

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

The products of Accelrys are:

* 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.