Pathway Prediction System | PredictBT Workshops | Biochemical Periodic Tables

About the Pathway Prediction System






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Return to Top Overview

The UM-BBD Pathway Prediction System predicts microbial catabolic reactions using substructure searching, a rule-base, and atom-to-atom mapping. The system is able to reconize organic functional groups found in a compound and predict transformations based on biotransformation rules. The biotransformation rules are based on reactions found in the UM-BBD database.

The pathway prediction system can be accessed at the UM-BBD Pathway Prediction page, which can be reached from the "Pathway Prediction" link on the UM-BBD home page, or by using the following URL: http://umbbd.msi.umn.edu/predict/.

The PPS predicts biodegradation of user compounds. Biodegradation of some types of compounds should not be predicted. Users can choose if they will view all or only the more likely aerobic transformations. The PPS uses Chemaxon's MarvinSketch and MarvinView Java applets as plugins. A user enters a compound into the system by one of two methods: Drawing the Structure and Generating SMILES or Entering SMILES Directly.

PPS Main Page

Return to Top Demonstration

The PPS provides a demonstration of how the system works using the compound Benzyl Alcohol. To access the demo, click on the "Demo" button located under the MarvinSketch window of the UM-BBD Pathway Prediction Page.

Press Demo Button

The Smiles string of Benzyl Alcohol will appear in the "Smiles string" box.

Smiles string appears

Return to Top Pathway Prediction Results

The system will automatically bring the user to the Pathway Prediction Results page for Benzyl Alcohol. The default setting for the PPS is "Aerobic" which will show the biotransformations most likely to occur in under normal conditions (exposed to air, in the top layers of water or soil). You can change this setting at any time to "All" as described under "Aerobic Likelihood" below.

From the Pathway Prediction Results page, a user is able to see the more likely aerobic transformations of Benzyl Alcohol based on the biotransformation rules found in the UM-BBD. The Navigation Bar "BBD Home > PPS Home > 1" permits quick navigation between different PPS prediction levels and the PPS and BBD home pages.

Pathway Prediction Results1


Return to Top MarvinView

The user can click on any grey compound square, either in "The predicted pathway", or "Choose the next reaction step".

Double-click any grey box


This will show the compound in a new window.
MarvinView window appears


The compound can be rotated in this window. The window can also be increased in size, to better view larger compounds. Double clicking in this new window will produce a MarvinView window. The MarvinView window can provide much additional information on the compound. Information on how to use it is available at http://www.chemaxon.com/marvin/chemaxon/marvin/help/view-index.html.

Return to Top Aerobic Likelihood

Aerobic Likelihood is the likelihood that the reaction will occur under aerobic conditions, exposed to air, in soil (moderate moisture) or water, at neutral pH, 25°C, with no competing or toxic other compounds. Rules are assigned aerobic likelihood by two or more biodegradation experts. More information is available.

The aerobic likelihood of a compound is displayed as a vertical colored bar on the leftside of a compound. A key is displayed beneath the compound undergoing transformation. The compounds are displayed in order of increasing aerobic likelihood.

A user is able to choose, before or after a compound undergoes transformation, if they will view all or only the aerobic likely transformations of a compound by selecting the appropriate button.

When the aerobic setting is used, an "immediate" feature is activated. All very likely and some likely biotransformation are acted on immediately, without manual intervention. The prediction process appears to skip one or more steps. All steps are shown in the predicted pathway.

If the aerobic setting is chosen, and no very likely, likely, or neutral transformations, but some unlikely and/or very unlikely transformations, are found, the setting is automatically changed to "All" and these transformations are shown.

Aerobic Likelihood 1


Return to Top Rule Button

The demo provides the user with the ability to click up to three buttons for each transformation. One of these, always shown, is the "Rule" button.
Rule Button


Clicking the "Rule" button will open a new browser window containing the rule page of the biotransformation rule associated with the specific reaction. The Biotransformation rule page provides a user with links to the PPS, a list of All BTrules, and the UM-BBD Main Menu. It also provides one or more descriptions of the type(s) of reactions handled by the rule, the likelihood the reaction will occur under aerobic conditions, a list of UM-BBD reactions that exemplify the rule, staff comments, similar biotransformation rules (if any), and a way for the user to provide comments. A list of all rules the system uses is available. More information about BTrules is available in About the BBD.

Rule Page


Return to Top Cpd Button

Another button is the "Cpd" button, located in the top right corner of an individual transformation beneath the "Rule" button. The "Cpd" button does not appear on every transformation (only on compounds found in the UM-BBD).

The Cpd button


Clicking the "Cpd" button will open a new browser window containing the compound page of a biotransformation. The compound page provides a user with a graphic image of the compound, its chemical formula, molecular weight, SMILES string, and links to reaction pages in the UM-BBD where the compound is either the substrate or product. More information about compound pages is available in About the BBD.

Setting the Reaction

Return to Top Next Button

Another button that is always shown is the "Next" button. The "Next" button is located in the top right corner of each transformation above the "Rule" button.

Next Button


Clicking the "Next" button brings a user to the Pathway Prediction Results page for that transformation. The biotransformed compound the user selected will appear as the second step in the predicted pathway at the top of the page next to the original compound. The colored arrow indicates the aerobic likelihood of the biotransformation that connects the two compounds.
Second Pathway Step


To continue the pathway, select the "Next" button on another transformation. The Navigation Bar will then expand to "BBD Home > PPS Home > 1 > 2" for easy navigation to previous PPS prediction pages or BBD or PPS Home pages.

Return to TopGreen Next Button

After several cycles of the prediction process, you might see a green-shaded version of the "Next" button.
Green Next Button


This indicates that this compound is readily degraded. If you click on a "Green Next" button, your predicted pathway is completed.
Complete Prediction


Alternatively, you may choose to contine prediction by clicking on a non-green "Next" button, if one is present.

Return to TopVariable Aerobic Likelihood

Some rules handle a wide range of compounds, and a single aerobic likelihood is not appropriate for all of them. Thus structure-based variable aerobic likelihood has been added to the PPS. For aerobically likely aromatic ring monooxygenation, ring dioxygenation, ring cleavage, and ring decarboxylation rules, when the substrate contains one or more halogens, the aerobic likelihood for the transformation is changed to "neutral". This is the first step toward better handling of aerobic likelihood.

Compare the previous predicted pathway for benzyl alcohol, with the pathway below for p-chlorobenzyl alcohol. The aerobic likelihood for the first three transformations are likely, as above. However when the ring is oxygenated and cleaved, the aerobic likelihoods are neutral for the chlorinated compound, rather than the likely found for the non-halogen.

variable aerobic likelihood



Return to Top Drawing Structures

The PPS uses Chemaxon's MarvinSketch for drawing compounds. To draw Benzyl Alchol in the MarvinSketch window, select the "Benzene Ring" from the lower tool bar menu. Drag the structure to the desired location in the window and click to paste. Next select the "single bond" button from the left tool bar (for more options e.g. double bond, single bond up, etc., click and hold the "single bond" button). With the "single bond" selected, click a corner of the bezene ring, drag the bond in the desired direction and release to paste. With the "single bond" still selected, click the methyl group, drag in the desired direction, and release to create a two carbon chain. To make the compound an alcohol, select the atomic symbol for oxygen, "O", from the right menu bar. Click on the methyl group to replace it with a hydroxide. For further information, a tutorial for using Marvin Sketch is available at http://www.chemaxon.com/jchem/marvin/chemaxon/marvin/help/about-sketch.html.

Drawing a Compound

After creating an image image in the Marvin Sketch window, a user must generate the SMILES string for that specific compound. To generate the SMILES string, click the "Write SMILES" button located beneath the MarvinSketch window.

Writing SMILES string

The SMILES string will appear in the window directly underneath your structure.

SMILES string appears

Click on the "Continue" button to proceed to the Pathway Prediction Results page for Benzyl Alcohol.

Return to Top Entering SMILES Strings

If your brower cannot run Java applets, or you have the SMILES string for your compound, you can instead enter a SMILES string. A SMILES string is an alphabetical representation of a compound. The SMILES string format is described on the SMILES Home Page from Daylight Chemical Information Systems, Inc. Type or paste the SMILES string of Benzyl Alcohol, OCc1ccccc1, into the "Smiles string" window.

Entering SMILES string

Click on the "Continue" button to proceed to the Pathway Prediction Results page for Benzyl Alcohol.

Return to Top For Further Information or To Make Comments

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April 07, 2008 Contact Us 

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http://umbbd.msi.umn.edu/predict/aboutPPS.html