newsletter #07 — Q4/2005

Welcome to the Santa Claus edition of the BioSolveIT newsletter

In our newsletter we publish information of new developments, events, milestones, and scientific facts on a quarterly basis.

successful completion of 3rd FlexX Docking Workshop

This year's FlexX Docking Workshop (following on from the two previous ones in 2003 at the ZBH in Hamburg and in 2004 in Princeton, NJ, USA), took place on November 10 and 11 at the Center of Advanced European Studies and Research, caesar (, located in Bonn, Germany. 26 people registered to learn more about our most popular docking tool. In two days, participants from 7 different nations, from novices to advanced users, were shown FlexX's innermost details, parameters and settings, as well as loads of tips and tricks on how to make the most of FlexX.

This year special emphasis was placed on the new features of Release 2, such as the new ligand initialization specified in the new static_data file transform.dat. In about 20 exercises, the participants were able to apply the previously learned material and deepen their acquired knowledge. One participant commented: A very intense and useful training on FlexX and all its parameters.

They worked on 26 brand new Opteron workstations sponsored by SUN Microsystems which ran the recently ported 64 bit version of FlexX. This version has an increase of speed of about 30-40% compared to the Linux 32 bit version. We will publish the results of a benchmark test yet to come in a later issue of this newsletter and on our website.

The next FlexX Docking Workshop will be close to the fall ACS meeting in San Francisco. Interested participants can pre-register for this event. They will then be sent updates and news about this workshop. We urge you to make use of this offer and as another participant this year put it: I believed I was an expert. Now, I do not, but I now know how to become a FlexX master.

FTrees goes web

In collaboration with our scientific partner the Center for Bioinformatics (ZBH) of the University of Hamburg, BiosolveIT is proud to announce web access to its rapid descriptor technology FTrees. The use of FTreesWeb is free of charge. Here, the FTrees descriptor is built into an easy-to-use query tool for quick similarity searching of a single compound against a selection of different libraries. FTrees compares molecules based on an alignment while avoiding the necessity of dealing with conformational flexibility. This makes it a highly efficient tool for similarity searching facilitating virtual HTS. The ability to detect novel molecular scaffolds is one of several features special to FTrees.

Here is how it works:
The web interface takes SMILES as an input. The user can choose to interactively draw the molecule of interest with Peter Ertl's Java application JME, or to simply cut'n'paste the SMILES string. In FTreesWeb a few compound libraries are pre-installed, among them the widely known lead-like subset of the ZINC compound database by Brian Shoichet. A maximum of 50 compounds can either be displayed on a results page or sent to you via email.

We invite you to explore additional options yourself at:

Help buttons '?' give quick access to short descriptions of the different selections, options and algorithms. More technical details about the underlying search engine can be found on the FTrees web page. As always we are interested in your feedback. Please email any complaints or suggestions to Obviously, positive feedback is also welcome.

Please bear in mind that this is the first version of FTreesWeb, so it should be considered a broad beta test. Especially the expected workload of the server is difficult for us to estimate. If the response time is high, especially at peak times after announcements like this, we recommend you checkmark email as the response mechanism and return to using FTreesWeb interactively later. You can also do this while the computation is running.

new zero-paperwork test licenses

Get faster access to BioSolveIT tools for testing! BioSolveIT is now offering test licenses for selected products. Starting with FTrees, the interested user can click through 5 different steps to obtain a test license which is then valid for two weeks. Other than the limited time-frame, test licenses are no different from regular licenses, so you can directly assess the benefits of the software. Christian Lemmen, CEO, explains the reasons for offering this third kind of license: With the test license, we would like to make it easier for the user to obtain BioSolveIT tools for testing — the trial software is now just a few clicks away, with no paperwork in between. License agreements for an evaluation copy valid for longer can be processed while the scientist is already testing the product. Try out the software while your lawyers still brood about the agreement!

Here's how it works:
In the first step, the user enters some personal information. At least an email address is required, as the license key for the software will be sent to this address. The next two steps require agreeing to the privacy protection and usage-regulations, followed by the determination of the CPU-ID. This is necessary, as the test license is bound to a specific machine. In the last step, you may review and need to confirm your data once more. Subsequently our system will send an email with the requested license keys valid for two weeks. Also, an evaluation license agreement will automatically be sent to you after one week. It is up to you to use it to request a standard evaluation copy if you want to proceed with the evaluation beyond the two weeks.

tips and tricks from the world of FlexX

Following established tradition, in this section we focus on aspects of FlexX that are either not very well known or are sometimes misunderstood, so we see them as important points to bring to your attention.

This issue will bring you more detail about directional pharm constraints. Using pharmacophore constraints you can significantly enhance the result of a docking, if you know how to use it correctly. See for yourself in our example.

If you have any questions or know of any tips and tricks yourself that you would like to share with the FlexX user community, we would appreciate your input at

BioSolveIT news in brief

Industry co-operations: Read more about an exciting project with Boehringer Ingelheim Pharma GmbH (Biberach an der Riss, Germany) during which FlexX-Scan will be developed, a FlexX with drastically improved performance for ultra high-throughput docking.

Prof. Matthias Rarey won this year's Hansch award from the QSAR and Modelling society.

Dates for your calendar

  • December 5-6, 2005: IQPC in London, UK: BioSolveIT will be present at this year's Virtual Screening and Lead Identification Conference. Dr. Marcus Gastreich will talk about
    Million Compound Docking – FlexX-Pharm and the Combinatorial Efficiency Boost
  • December 16, 2005: Tripos User Group Meeting, Tokyo, Japan and Seoul, Korea (December 20): Dr. Carsten Detering will talk about
    The Next Generation Docking Engine: The Single Interaction Scan

Availability of our latest conference presentations

  • September 9, 2005: Dr. Marcus Gastreich talked at the MGMS International Meeting about
    Combining the efficiency of combinatorial chemistry with the power of pharmacophore-based docking

All available BioSolveIT talks can be found in the conference section of our website.

literature corner

  • A Critical Assessment of Docking Programs and Scoring Functions
    G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, and M. S. Head
    J. Med. Chem., ASAP article
    details here
  • Improved FlexX Docking Using FlexS Determined Base Fragment Placement
    S. S. Cross
    J. Chem. Inf. Model. 45, 993-1001 (2005)
    details here
  • Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols
    A. Evers, G. Hessler, H. Matter, and T. Klabunde
    J. Med. Chem. 48 (17), 5448-5465 (2005)
    details here

upcoming articles

  • Exciting news about the Docking Database (DDB)
  • Performance data of 64-bit FlexX


stay tuned with all the breaking news.


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