Here we have collected some of the most important questions regarding user issues, along with their answers. We have separated the user issues into the topics listed below. We apologize for the length of some of the answers given, but this is necessary due to the need for complete responses.


The MetabolExpert print-out creates a lot of paper, and is very inflexible. Is it possible that I have not found the right settings?

We have tried to develop a flexible way of printing "metabolite-trees", but this poses many questions on this solution. The default appearance of metabolite-tree is optimized to the screen display. The dashed lines represent the edges of the each paper sheet. To modify the size of printed structures you have to use the expand and shrink buttons (plus or minus symbol in a rectangle). The zoom in/out button has a similar appearance (plus/minus symbol in a magnifier), but only zooms the screen, and does not modify the size of the printed structures. You can even move the structures by drag-and-drop. With shrinking and arranging of the structures, you can compact the result into a few sheets of paper.

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Ideally I would like to process SD files in batch. Is this possible with your software?


There are some possibilities for this purpose.

  • A real batch prediction is possible in the Unix version. You can run the prediction on your SDFile, and the results are either displayed on your screen or saved to an output text file.

  • In the Windows version you can import your SDFile into a compound database, then predict all of the structures at once. (You can then export the results to delimited text file(s).)

  • With the DLL version you can solve this problem even on your inhouse database, probably without having to export your structures to SDFile. The DLL version is easy to parameterize, so it can be implemented to many different database (e.g. SQL-Access combination, etc.)

  • We have already released Pallas Plug-in for ISIS(TM), and if you store your compounds in ISIS, this add-in makes you able to calculate the physico-chemical parameters of your compounds automatically.

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As many of the compounds we deal with are charged and zwitterionic, any package we buy must have support for calculating these groups. Does ProLogP offer support for charged species (phosphates, carboxcylic acids, ammonium compounds, e. g. Phosphoryl choline) ?

PrologP converts any charged compounds to the neutral form, whenever possible. For example, if you have a compound having a charged carboxylic group, the structure will be converted to the protonized form, and if you have an amino acid, it is represented in its uncharged form. Naturally, the program will calculate the logP value with taking the charged species into account, so the result will be the proper logP value. If you are interested in the logD value corresponding to the dominance of a given charged species, you can use PrologD instead.

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As I understand, the fragment data of HazardExpert is based on the US EPA. Can we get this data?

Unfortunately we cannot give out this information due to confidentiality reasons, but we can give you the source of the report. Please try to obtain it yourself:
Brink. R.H..J.D. Walker: EPA TSCA ITC Interim Report.
Dynamic Corporation, Rockwille, 6/4/1987

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Do you validate from the US EPA data in making your knowledge base? For example, when making the toxicity of a fragment. Did you validate the toxicity of the fragment only, or the toxicity of compounds including the fragment?

Yes, we have validated the data in the interim report upon its first inclusion into HazardExpert. The result was that some fragments were missing; therefore we further developed the knowledge base with a collection of additional fragments (from the literature). Since the first EPA interim report dealt with fragment indication in toxic compounds, the toxicity of a fragment corresponds to the toxicity of the compound where this toxic fragment rule had been extracted from. When finding more than one toxic fragment in a compound, the predicted toxicity is equal to the toxicity caused by the most toxic fragment.

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Percentages of each toxicity class are present as result. What do these percentages mean?

The toxicity is predicted on a 0-100-percentage scale in each toxicity class. It is a kind of probability of toxicity in the given class. Since this number is not a very precise value, the final result is given in probability categories as follows:

  • Highly probable toxic
  • Probable toxic
  • Possible toxic
  • Uncertain toxic
  • None toxic

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At first, you divide five classes by percentages of each toxicity. Do you have a good reason for this division? Why did you set 60-100% to highly toxicity? Is this authorized?

No, it is not authorized. This is an approximation. Since the toxicity prediction included in HazardExpert is somewhat qualitative rather than quantitative, we had to translate the result given in the 0-100 scale to something that was easier to understand for the users. So, as a final step, we convert the highest toxicity value to a classification type, and the overall result - besides the bioavailability and bioaccumulation - is a probability level of toxicity.

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Does HazardExpert evaluate the logP value of the compound in question, along with its toxicity? With the Demo version I only tried to install HazardExpert and MetabolExpert, and when I see the results of toxicity, there are always logP and pKa values present?

Yes, HazardExpert predicts the pKa and logP values of the compund, and uses these for calculation of bioavailability. On the other hand, the details of pKa and logP predictions cannot be displayed and the values cannot be exported. To be able to do that you have to install pKalc and PrologP.

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When using HazardExpert, I noticed that when a compound is not toxic there are no results shown even for logP and pKa.

It is true. The results are shown only if at least one toxic fragment has been found. The bioavailability data - and therefore the pKa and logP values - is a part of the results, and important only in the case of a found toxic symptom. If there is no toxic fragment in the compound, the bioavailability will lose its meaning in the toxicological point of view.

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How big is the HazardExpert database?

It contains approximately 100 toxic rules. Every rule corresponds to a toxic fragment with many different structural conditions for the neighboring atoms, and the appropriate toxic effect is assigned to the specific toxicity class (such as oncogenicity, mutagenicity, etc.). So every rule is globally defined, and usually is a collection of more toxic symptoms.

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Does a single license mean that you can install the software on one computer and access it from there, or does it mean that you can install it on a network and only one person can access it at a time?

Single license means that you can install it on only one, individual computer. For network use purposes you need the network version, which is a kind of client-server type (LAN, Win NT): the main program is install on the server, and you can install as many clients as the number of users purchased. The installation/uninstallation of clients is very fast though, so it does not mean that you have to use the program always from the same computers. Instead, the number of installed clients at the same time is controlled, so if you buy a network version with 5 clients, then the program can be used from 5 computers at the same time.

Write to our technical support.

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