Once you open the job results page you have a header section allowing to browse through different aspects of the data that has been produced.
Click on Overview to open the overview tab. This page allows you to plot 4 key properties derived from this paper.
You'll see histograms of distributions for :
1. Hydrophobic Patch Areas near the CDR
This is the largest hydrophobic patch closest to the CDR measured in
2. Antibody CDR Length
This is the total amount of amino acids composing the CDR loops
3. Fv Charge Separation
This is the difference of net charges between the heavy and light chain
4. Ensemble Net Charge
This is the overall net charge of the full Fv - linked to viscosity & clearance.
During an analysis of hundreds of clinical stage therapeutics (CST, phase-2 or later) average property distributions of Fv's have been analysed. As a result property distributions for these reference CST antibodies are known. For each of these properties we show theoretical boundaries derived from this CST analysis for Fv's. For instance, hydrophobic patch areas near the CDR have an upper limit of
The aim of this analysis is to provide a quick overview of larger screening jobs vs this reference data. Statistically, infringement one or more than one of these rules & boundaries lowers the chance of passing approval by 50%.
Fv Boundaries & properties
Hydrophobic Patch CDR
Upper boundary:
Antibody CDR Length
Lower boundary: 61
Upper boundary: 75
Fv Charge Separation
Lower boundary: -4
Upper boundary: 4
Ensemble Net Charge
Lower boundary: -2.5
Upper boundary: 8.5
Limitations
These boundaries have been derived from public domain literature analysis and are only valid for Fv or compatible fragments.
Comparing to a different reference
In case you have a different modality or you want to set your own boundaries there are two ways to adapt this analysis for you.
Compare to an existing reference calculation
If you have set up your own reference space calculation for your modality, i.e. VHH you can also show molecules of a previously run calculation in the overview tab as well. Click on the "Global Properties" tab in the navigation bar. On top right section you have a box looking like this.
Click on it and it'll show all collections of molecules you have set up in your system. If nothing show up you need to first create a collection in 3dpredict/Ab. Refer to the Collection documentation on how to set this up.
Once you selected your reference collection, click on the overview tab again.
You should see your current job in purple and the distribution of the reference collection you just added. Here's an example:
. The green distribution is the one from a custom reference job added to the overview.
Adjust boundaries
If you want to permanently set your own boundaries for your application, the power user of 3dpredict/Ab for your tenant can set these as well. Click on the cog icon in the left navigation bar. Then choose Histogram Parameters
This opens up a configuration page allowing you to adjust, which properties to show, the chart titles, axis labels, binning details for the histogram and boundaries as well as colours.
For example I want to adjust the properties for VHH's, click on the Edit button in the top center. This puts the table in edit mode.
When clicking on the first property name field in the VHH section you'll see a multiple choice box popping up. You can choose your property of interest here.
Below here you can see an example where I added pI3D and the total polar solvent surface area as an example. I added the ranges of values I consider to be observed as minimum and maximum and the binning width that should occur. The Cutoff Min and Cutoff Max are the boundaries that will be indicated to the user.
Click on the save icon on the top to persist these customizations. NB: these changes are visible to all users that have access to 3dpredict/Ab in your subscription. So this should be done as set up from power users.
Here is the final output of the boxplot for a job on a single VHH, we can see our boundaries and the color settings we chose.