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AKos GmbH Newsletter

 June 2015

Complete chemical information system
Advertise in iScienceSearch
Proteax® - easy interchange of full structures and three or one letter codes for peptides
Consulting for biological registration systems
Special Offer: screening compounds
Database of unpublished experimental results of 50’000 agro chemicals
Scilligence Chemoinformatics Development Suite
Academic package: electronic lab journal (ELN)
Substructure searches in AKosSamples
Complete chemical information system














AKos GmbH and Biochemfusion developed a chemical database system based on RDKit and PostgreSQL. This is a multiuser system.

  1. Are you unable to grow your ISIS/Base system because you have reached the size limit?

  2. Are you unable to share your data with a true multi user chemical information system?

  3. Are you unable to export directly to Excel?

  4. Are you unable to improve the quality of your data, like correcting structures, names, and CAS Registry Numbers automatically?

  5. Are you looking for a full chemical information system that can run on both on a server or on your local computer?

As a supplier of chemicals you might have experienced the following issues:             

  • You are unable to get quickly a list of potential suppliers for a chemical.

  • You want build your own web shop with the ability to search your compounds by substructure and similarity.

  • You want to know the prices for your compounds from other suppliers.

We offer a database system based on PostgreSQL and RDkit that works under Linux, and works very well in a virtual machine under Windows. The client can be installed on Linux or Windows.  

We offer as a standard interface to other systems the registration of SDFiles. We support ChemDraw and ISIS/Draw. The supported virtual machines are VMWare and HyperV. 

The price for the system is 5000 Euro per year for a company, irrespectively of the number of users.

Would you be interested in services, and/or would you be interested in having your full chemical information system. 

Please send an email to:

AKos GmbH




















The standard import functionality and the standard data dictionary might not be what you want. We offer services to adjust the system to your needs. We have a lot of experience cleaning your data before we register them into the system: 

Structure checker: This application checks the correct valence, weeds out wrong structures

Standardizes structures, for instance converts 5 valence nitrogen in 3 valence nitrogen (e.g. uncharged nitro groups gets converted in charged nitro groups)

Name checker: This application is able to correct errors in names, i.e. if words are spelled wrong like immidazole instead of imidazole. Such a correction cannot be 100%, but it finds many errors.  

CAS number checker: This application checks if the CAS Registry Number is a valid CAS number. It finds incorrect assigned CAS numbers. Often the CAS number given is in reality for a salt and not for the parent. We only have access to CAS numbers that are in the public domain, but this are already quite a lot.

Data enrichment: This application can add

  • Synonyms

  • CAS Registry Numbers

  • IUAPAC names

  • PASS parameters (predicted biological activities)

  • …and more

to a compound record.


For certain customers we have applications that provide data directly:

Names of potential suppliers for a certain compound. You would like to give some identifier like synonym, CAS Number, AKos Number, IUPAC name, etc. and get quickly a list of suppliers.

Get quickly the prices for compounds from other suppliers.

Biochemfusion has a long experience on building systems for peptides. The system can be extended to handle peptides sequences with structure modifications.

Would you be interested in services, and/or would you be interested in having your full chemical information system. 

Please send an email to:

AKos GmbH


How can I search Google with the chemical structure?

Advertise in iScienceSearch

We decided to finance this project by advertisement. It is free for everyone. Please see our advertisement prices at advertise.htm. They are vey low!

Advertise with iScienceSearch



Search for structure-modified peptides 

Proteax® - easy interchange of full structures and three or one letter codes for peptides

Biochemfusion's Proteax software suite makes it easy to handle modified proteins and protein derivatives. Use Proteax with Microsoft® Excel® or Oracle® databases to register and analyze your protein structures.

The chemically-aware Proteax engine enables you to work with post-translationally and chemically modified protein sequences. Protein data can therefore be transferred directly to bioinformatics tools, chemistry tools and to and from mass spectrometry instruments.

Proteax is included in iScienceSearch and is the first application that makes is possible to search  and analyze the results for structure-modified proteins.


Benefit from the know-how of specialists 

Consulting for biological registration systems

Dr. Jan Holst the producer of Proteax and owner of BioChemFusion can help you building a biological registration system. He and other from ( have the experience and know-how to build systems. 



and more years experience in chemoinformatics of each person

Low cost offer of a screening compounds 
















Special Offer:

Several of our suppliers offer larger collections for a very attractive price. We supply 5 mg of dry powders in vials or well-plates. Shipping cost is 150 € to Europe and 200 € to USA, of course, in the case of big order we'll send free of charge. Below is only one example of such a special offer.
The files contain ca. 12000 structures. We also extracted the scaffolds using the KNIME Murcko node. We have added the PASS parameters to the download files. This enables you, not only to select your molecules by structure, but also by estimated biological effects (toxicities, gene expressions, etc.)





AK_final with Lipinsky (PASS12)_sdf.7z

8,0 Mb

Excel file with SMILES

AK_72 PASS effects and Lipinsky_xls with smiles.xls

16,5 Mb

Excel file with structures. You need ISIS for Excel to work with this file.

AK_72 PASS effects and Lipinsky_xls for ISISforExcel only.xls

35,5 Mb

ISIS/Base database

AK_11809 cmps with Lipinsky and PASS ISISBase db.7z

7,9 Mb

Instant JChem database (Murcko scaffold are included)

12k screening cmpds Instant JChem db.7z

25,3 Mb

SDFile of extracted Murcko Scaffolds

AK_deduplicated Murcko_sdf.7z

0,5 Mb

ISIS/Base database of the Murcko scaffolds

AK_Deduplicated Murcko ISISBase db.7z

0,5 Mb

You can download the files either by clicking on the link, or using the ftp download, see



Save money by avoiding unnecessary expensive testing in green-house and field. 


Database of unpublished experimental results of 50’000 agro chemicals

AKos GmbH is reselling a databases of ca.  50’000 compounds and ca. 1’000’000 test results. The compounds are potential herbicides and fungicides. The rights to these data were rightfully acquired when the LEUNA group of companies were dissolved and sold. Many of these data have importance for REACH, and research. The data were very unstructured and were recently reworked into XML files, ACCESS database and the structures are in SDFiles. 

1 Million

unpublished test results



Cost effective chemoinformatics suite 











Scilligence Chemoinformatics Development Suite
DevSuite, is a complete toolkits for developers to build web applications and .NET applications.  Dev Suite contains following key modules:


JSDraw - 100% Javascript Chemical/Biological Structure Editor


JSDraw.WebServices - JSDraw server side web services to extend JSDraw capabilities


MolEngine - .NET Cheminformatics Toolkit


MolEngine.Plugins - Third-party modules to extend MolEngine capabilities


MolSql - Chemistry Cartridge for Microsoft SQL Server

To download DevSuite or individual modules:


Please send us an email to to schedule a demo, begin an evaluation, or request further information.



What happens when I want to change the vendor?

What happens when I need to use my own server, due to security reasons? 



Academic package:
electronic lab journal (ELN)

Many professors would like to use an ELN. However, they work with companies and they use paper notebooks due to security reasons. They are not allowed to put anything in the cloud.

The other issue is what happens to the data, if they want to change the vendor?

AKos GmbH and Scilligence agreed to offer a solution where you can use the Scilligence software on your own server. You still can use the cloud, if you prefer. If you decide to terminate the agreement, you will get a SQL database package with your data.

Onsite ELN Academic Package up to 20 users: License fee 250/user – 5,000 Euro annual (includes maintenance), 10000 Euro perpetual (20% Annual Maintenance fee)
Installation and training  2000 Euro + expenses

Please send us an email to to schedule a demo, begin an evaluation, or request further information.


Euro per year plus 2000 Euro installation


How can I search in AKosSamples?


How to search in AKosSamples?

You can search by full structure, substructure and similarity in many database in iScienceSearch. One of these databases is AKosSamples.

>25 million

structures are in the AKosSamples database. About 6 million samples are on stock.


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