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Consulting & Solutions GmbH
a chemoinformatics company


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Home Up News0708 News0409 News0610 News0810 News1010 News1210 News0611 News1011 News0415 News 0412 News0413 News0615 News0915AKos GmbH Newsletter October 2010

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


Analyzing and working with Proteins

Proteax - protein variants made easy

Compound suppliers and sellers of chemoinformatics software

CWM Global Search - a place for advertisement

Any chemist and biologist

Example what you can find in CWM Global Search

Scientist searching for compound suppliers and procurement officer

SCD (screening compound database) is added to ACD on the All New DiscoveryGate.

AKos Samples is now updated in other public database. AKos Samples data source is updated in CWM Global Search. This works also in the free version.

Medicinal chemist, in silico screening

CWM Lead Finder enhances working with PASS - increase the accuracy of prediction

Group leader and project manager involved in an IT project

GxP Manager - a program that helps you to break large IT projects into manageable parts

Any chemist

Accelrys Draw 4.0 is released - get a free version for academic and non-commercial use.

Confirm or reject future newsletters

Our mailing list is generated mainly from business correspondence. We use automatic procedures to do this.

Please send an email to subscribe@akosgmbh.de if you want to receive future newsletter, or send an email to unsubscribe@akosgmbh.de if you want to be removed from the mailing list.

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

AKos GmbH added the products of biochemfusion to its portfolio.

Proteax is a program that is used by researchers that have to make structure modifications on proteins. You can generate both structures and sequences, enabling you to do a substructure search, for instance in Isentris, and also a sequence search.

You can also do calculations with your protein right inside Excel. All the calculations are functions that you can choose like any other Excel function, like "sum".

You can even use these functions in SQL queries using the Proteax Cartridge.

These functions are extremely useful for identifying different protein modifications.

For those who don't work with proteins. Why would one modify proteins? You can modify insulin, so it becomes less soluble and is then absorbed slowly. This is the type of insulin that you will take in the evening, and it will last all through the night keeping your blood sugar stable.

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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 44 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. 

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.

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


Place your advertisement in CWM Global Search. This will help us to keep the price of the application low, maybe even free one day.

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Examples of

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You want to know something about "mephedrone". This is a designer drug.

In addition to references found in SciFinder:

*        You can buy 25 mg of mephedrone for 110 USD at a company in Toronto, http://www.trc-canada.com/detail.php?CatNum=M224200

*        You will find an article: "

Mephedrone: an update on current knowledge",  http://www.drugsandalcohol.ie/12762/

*        In Google Books is "The Learning Mentor's Resource Book?"  - Page 118 (Slang terms for Mephedrone. Next time you are in Amsterdam and someone offers 'Bubbleluv', you know what it is. http://books.google.com/books?id=2_V4HS7qYKIC&pg=PA118&dq=mephedrone&cd=6#v=onepage&q=mephedrone&f=false

*        CTD - Diseases associated with Mephedrone

*        NovoSeek - found as 4-methylmethcathinone  a synonym for Mephedrone (from Wikipedia)

*        You find spectra: http://forendex.southernforensic.org/uploads/spectra/mephedrone_expanded.pdf

*        http://www.fsijournal.org/article/S0379-0738(09)00549-0/abstract

*        ... and more articles in Medline and citation in Google Scholar.




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Make informed compound purchasing decisions and cut costs with structure-searchable databases of supplier compound information that include supplier, location, package, purity, and cost information. The SCD (screening compound database) data are now added to the web application of the All New DiscoveryGate.

Go to www.discoverygate.com/dg3 and the ACD/SCD application opens. If you have no login information, you still can use it, only, you will not see prices and the shopping cart will not work. You can ask for a free-of-charge evaluation.


CWM Lead Finder is an extremely powerful tool to quickly find lead compounds in a large set of compounds with unknown biological effects.

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Results of comparing PASS with CWM Lead Finder.

Cluster or Pa value

Compounds with the activity "antiinflammatory" in CMC, the so-called "Knowns".

Number of "Knowns" in the hit list

Total number of hits

Maximum number of false-positives

All compounds





Clusters ratio >1





Largest cluster





Largest ratio 





Best ratio (15%)





PASS 2009 Pa>Pi





Pa >0.9





Pa>0.4  best





*        PASS gives the best ratio of actives versus false-positives at Pa > 0.4 - We have no idea if this is general, but we observed it several times.

*        CWM LF provides already a significant enrichment taking all cluster with more than one known, and loses very little potential positives. CWM LF performs better compared than PASS for activities that are not so well represented in PASS. (PASS predicts all "antiinflammatory" compounds" in CMC with Pa>Pi. This is a good result, but this is expected since all compounds are part of the knowledge base.)

*        CWM LF provides very potential leads in the clusters with the greatest ratio (high accuracy) - this is why CWM LF was developed.

*        Pa > 0.9 provides also high accuracy, but in CWM LF the user has additional clusters if the structure similarity compared to known compounds is too large.

*        CWM LF provides an easy user interface to compare known and unknown.

*        CWM LF performs better when the profile is made by ca. 20 activities, but basically it is not very sensitive to this. 

*        CWM LF has further selection methods for finding the best lead using structure similarly clustering, toxicity warning, and sorting by PASS numbers (the larger the number the less specific is the compound).

*        The approach of using biological profiles instead of single activities has been proven valuable.




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AKos GmbH is a broker for selling screening compounds.

*        You can search the AKos Samples database by structure using CWM Global Search.

*        Please visit our download page. All SDFiles were normalized, and have a consistent AKos Number. Please replace any previous files that you had from AKos Samples.

*        We also offer as service to develop syntheses for you. We have several labs that work extremely well and are suited for such tasks. 

*        You can hire a full term equivalent of a chemist to synthesize compounds under a secrecy agreement.

Screening compounds
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Telephone (Greta Auf der Maur) +49 7621 162 2778
FAX     +49 7621 162 2779
Please use the keyword "Beilstein" in the reference line to avoid the SPAM filters.

GxP Manager is a program that helps you to collect all the user requirements for an IT project. The software helps you, and forces you to translate these requirements to functional specification and technical specifications that are in accord to regulations.

You can validate modules, as they become available.

GxP Manager helps you to break a large project into manageable pieces, and provides you an overview at any time.

When analyzing the tasks in a validation cycle, one must recognize that the time taken by valued technicians to create paperwork largely exceeds the time to execute the tests. Paperwork may have to circulate multiple times before being approved. GxP Manager avoids all this paperwork during the process, only the final results are printed for documentation purposes.


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a software for IT projects!

Accelrys Draw 4.0 released.

Get no-fee Accelrys Draw for academic and non-commercial use

For Chemists—quick and efficient structure and query drawing

*        Structure converter converts structure-to-IUPAC name and IUPAC name-to-structure; structure-to-canonical SMILES and SMILES-to-structure; structure-to-InChI name and InChI name-to-structure; and structure-to-InChI key

*        Create and edit ISIS-compatible sketches, edit legacy sketches with improved cleaning of sketches

*        Ease the transition with familiar ISIS/Draw-like chemical drawing tools and behaviors

*        Create and edit polymers, formulations, and mixtures (Sgroups)

*        Create and edit Rgroup (Markush) queries including built-in Rgroup query logic

For Biochemists—draw, register, search and report on chemically modified peptide or nucleotide sequences

*        Create 1- and 3-letter peptide, DNA, or RNA sequences with a Sequence tool

*        Use the same tool to draw crossing bonds, disulfide bridges and attach side-chain protecting groups

*        Convert text from the clipboard, FASTA, Swiss-Prot, PDB, and EMBL files into chemically significant sequences

*        Expand residues in a sequence to full structure to illustrate chemical modifications

For Developers—Accelrys Draw no-charge add-ins offer fast, easy extensibility

Accelrys Draw's documented API enables developers to create custom add-ins and drop them in as tools, buttons or menu items. The no-charge add-ins include:

*        Molecular property calculation/prediction

*        Enumeration

*        Bioavailability

*        Isotopomer distribution tools

*        Stoichiometry calculator

*        2D to 3D converter


* 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.