3dpredict/Ab 2025.09

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This autumn release of 3dpredict contains several major updates in the platform.

1: Reference collections

When analyzing your job results you can now drag into your analysis previous jobs that you ran and use them as basis for comparison as well as positive & negative control data.

collections
In this screen you can define a set of molecule(s) from any job you have run before to build up a reference collection. By assigning the collection type to either: Positive Control, Negative Control or Neutral Reference you can then subsequently use them in your whole protein property reports to compare new results to these reference calculations.
collection
Once you added the collection to the whole protein properties table you'll see them pop up directly within your data colored by control type (red for negative control, green positive control & blue for a neutral reference).
collection
This allows you to directly sort/filter/compare/export & share results in light of common control molecules you use in your assays. These newly added collections to your report are available throughout all analysis tabs of your job, so you can for instance also easily compare sequence & structural differences.

Persistence Limitation

You can import a collection into your job during your current session and work with that. They are currently not persisted with the job data, so logging out and back in will reset the job data to its original state.

2: Support for ADC's & more

We've now opened 3dpredict also for property predictions of non standard antibody architectures, such as ADC's and other constructs. The current limitation is that you have to provide your own structure as input PDB or CIF the time being, but 3dpredict will run the pH dependent sampling protocol on these & provide all properties available if applicable. Here is an example of an Fc only - ADC:
ADC

3: Protein property plots

For the molecules in your protein properties table you have now a dedicated tab to do simple scatter plots of all properties available in the table:
property plots
Note that if you want to filter down on a subset of your set of molecules you can either select them in the protein properties table or select them in a given property range in the plot itself and they'll be synchroneously selected in the property table as well. So there's a neat bi-directional selection synchronization happening.

4: Residue property plots

residue plots
Here we have now added the possibility to generate easy comparison plots between different molecules on the residue level (projected to the x-axis). If you quickly want to check major changes of residue exposure or solvent accessible surface area, contributions to charged or hydrophobic surface patches, you can achieve this with a few clicks in this tab.

Feel free to add multiple molecules using the molecule selector in the top right of the window to set up the view the way you want it and all of this with the numbering scheme of your choice being used.

5: Multiple sequence alignment view

In the very same way as the residue plot and liability tables, the sequence & structure viewer allows now to pull in multiple structures & sequences and compare them between each other. This viewer is populated by the very same data you have available in tabular format in the residue property & liabilities tabs with additional information about patches in the structure.
sequence alignment

6: Condensed liability report

We now integrate a more condensed liability report than before where predictions from mutiple models for the same endpoint are collated to give a more streamlined & easy to analyze view of the data.
liabilityReport

7: Additional search capabilities

Once you start piling up jobs & calculations with different conditions & variants it will become complicated to recollect when you calculated what in which job etc.
In the job search dialog available here:
search1 you have now the possibility to add additional new filters (click on the filter + icon).
This allows you for instance to find jobs by CDR sequences.
search2