submission, this will open a new interactive window entitled
“which residue to mutate?”where the amino acids from the 3D
structure are displayed by chains using one-letter code and its
specific chemical structure scheme on the right side (seeNote 9).
By clicking each amino acid tab, a small popping window will
permit to select the desired amino acid from a scrollable list,
set alphabetically. Press “Save changes and submit”button to
finish the project submission and start the run; or “undo”button
to restore thewild typesequence (seeNote 10).
l Distance: Two resolutions, named “distance of aggregation
analysis,” can be used to run A3D. Maintain the default 10 A ̊
distance to disclose aggregation prone clusters on a structural
region. Change to 5 A ̊when dissecting the specific contribution
of each amino acid to an individual aggregation prone region or
inspecting the local impact of one residue (wild typeor mutated)
to close surroundings.3.3 Submitting
and Queueing
Press “Submit”button to start A3D calculations. The project will
be immediately moved to the queue list, accessible from the toolbar
“queue” tab, and the user will be redirected to a new page with the
project details and status (seeNote 11). The status of the user
project can be tracked in the queue list or in the project window
where it will change from: “pending” (orange) to “queue” (light
blue) and “running” (dark blue). If A3D encounters any incom-
patibility, it will be marked as “error” (red) and the developers will
be warned. As soon as the server would finish the task, the project
will be tagged as “done” (green) and A3D will inform through a
mail notification (optional). Only then, the user can access to the
full report of the prediction.3.4 Output
and Evaluation
of the Prediction
The A3D output consists of a set of four different interfaces.
Aggregation propensities are presented in a comprehensive man-
ner, incorporating the possibility to download data for a more
accurate evaluation of the results.3.4.1 Aggrescan3D Plot Probably the most extended and accepted representation of pre-
dicted aggregation propensities, where A3Dscoresare plotted as a
function of the amino acidic sequential position (Fig.3a). It can be
downloaded as a .png or .svg image file by opening “Download
plot” dropping window. By default, only the residues with A3Dscore
different from 0 are included; however, there is also the possibility
to show those residues even though they are predicted as non rele-
vant for aggregation. Finally, the interface allows the user to choose
which chain of the submitted structure, if several, is charted.
3.4.2 Aggrescan3D
Score
The score-table interface displays the numeric values of A3D calcu-
lations (Fig.3b), which can also be downloaded as .csc or .txt files.Predicting the Aggregation of Protein Structures 433