Two-Step Prediction
The images shown above are for a prediction done one step at a time.
Alternatively, two prediction steps can be done, one after the other.
All choices are the same or very similar; the process takes a bit longer than a single prediction, but not twice as long.
Chose "Two steps" at the PPS home page.
The results after clicking "Demo" are shown below.
Immediate rules are implemented a bit differently in two-step predictions.
Thus the Path 1 second step shown below is slightly different than the second step of the single step prediction shown above.
The transient benzaldehyde is replaced by benzoate in the second step choice for Path 1. However, if the next step is chosen from Path 1, the aldehyde will be included in the predicted pathway.
Duplicate products are also handled differently in two-step predictions.
If a duplicate product appears in single-step predictions, it indicates a prediction loop, and predictions stop at that point (the duplicate product is not shown).
In two-step predictions, duplicate products can appear in different paths, so must be shown. They are indicated by superscripts, and a legend at the bottom of the prediction choices indicates the compounds in each duplicate group.
This is shown below for the prediction for the pesticide Amitraz (CC1=CC(=C(C=C1)N=CN(C)C=NC2=C(C=C(C=C2)C)C)C).
There are three groups of duplicate products: 1 = compounds 1, 6, 11, and 12; 2 = compounds 3, 8, and 14; 3 = compounds 9 and 13.
The "Next" button is removed from a duplicate product that appears in a lower level if it also appears in an upper level. Look for it there.
Two step predictions may permit better analysis of the next choice.
For the two step prediction of the pesticide Amitraz, shown above, there are four very likely predicted compounds in the first step, formed from cleavage of the two formamidines found in Amitraz.
Compound 1 is 2,4-dimethylaniline; this compound has one neutral predicted biotransformation in the second step and would be predicted to accumulate.
Compound 2 (the second piece which contains the second formamidine) also undergoes very likely cleavage to produce 2,4-dimethylaniline (there is no Next button for it, since its degradation is shown in the first step).
The other three compounds in Path 2 are Compounds 7 and 9, readily-metabolizable small molecules, and Compound 8, which is predicted to degrade to 2,4-dimethylaniline, as shown in Path 3.
Path 4 contains 2,4-dimethylaniline, Compounds 13 and 15, readily-metabolizable small molecules, and Compound 14, which is predicted to degrade to 2,4-dimethylaniline as shown in Path 3.
Analysis of these four paths show that Amitraz is predicted to degrade to two molecules of 2,4-dimethylaniline (confirmed by experiment), and Compound 5 in Path 1 is the best choice to continue the predicted pathway.
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.
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 
