Green Next or Cpd Button
After several cycles of the prediction process, you might see a green-shaded version of the "Next" button.
This indicates that this compound is readily degraded. If you click on a "Green Next" button, your predicted pathway is completed by ending at the chosen compound.
At the same time, all branches ending at other compounds are removed.
In the example below, compound 6 and 8, not on the
path between compound 1 and compound 9, the chosen compound, are removed.
The "Green Cpd" button indicates that this compound is found in a KEGG pathway. Clicking the "Green Cpd" button brings a user to a KEGG pathway web page. Alternatively, a user may choose to continue prediction by clicking on a non-green "Next" button, if one is present.
Remove Products
As shown above, when the Next button is clicked, the new pathway contains that compound and the pathway branch or branches that produced it.
That is, other predicted compound squares and rule arrows are removed.
The "Remove Products:" option at the bottom of a prediction, allows more control over compound removal.
Compounds are removed by entering their numbers (the small number shown in the upper left of each grey compound square), separated by commas, in the "Remove Products:" box, and then clicking on the "Go!" button below the box.
The starting compound (compound 1) cannot be removed.
The (More) link will open this section of the UM-PPS help webpage in a separate window.
For example, above is the 3-level prediction for benzenesulfinate.
If it is desired to remove the compound benzene (product 3) in level 1, and phenol in level 2 (product 5), these compounds, and all compound boxes and rule arrows following them, are removed
by entering "3,5" (or "5,3") in the "Remove Products:" box, and clicking the "Go!" button.
The partial prediction is shown below:
To return to the original prediction, click on the "Show Original" button, to the right of the "Go!" button after a partial prediction has been made.
Once back at the original, you can return to the partial prediction by clicking on the "Show Partial" button, in the same position as the "Show Original" button.
Compounds in a partial prediction retain the same numbers as in the original prediction.
Since some compounds were removed, there are gaps in the number sequence.
Removing compounds can be done in multiple steps, without returning to the original prediction.
In the above example, you can get to the same result by first choosing to remove compound 3 (or 5),
and, after reviewing the result, choosing to remove compound 5 (or 3).
If you return to the original prediction, you can remove different compounds to create a new partial prediction.
If a previous partial prediction exists, the new one overwrites it.
Zoom In, Zoom Out, and PDF buttons all work in a partial prediction the same as in the original.
Clicking the Clear button in a partial prediction returns to the original.
Compound, Rule and Next buttons work in a partial prediction as in the original.
If the Next button is clicked in a partial prediction, the Next step in the prediction will be that of the original, not the partial, prediction.
Variable 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".
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 value found for the non-halogenated compound.
A second use of variable aerobic likelihood is for nitro groups. Aerobically likely or neutral rules for oxidation of aliphatic carbons have been changed to unlikely when the chain contains one or more nitro groups.
Super Rules
Super rules include two or more contiguous biotransformation rules that form a small pathway of their own. They are indicated with asterisk. For example, bt0055 and bt0351 are super rules shown on the Figure in "Variable Aerobic Likelihood" section above.
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/products/marvin/marvinsketch/.
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.
The SMILES string will appear in the window directly underneath your structure.
Click on the "Continue" button to proceed to the Pathway Prediction Results page for Benzyl Alcohol.
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.
Click on the "Continue" button to proceed to the 
