might result into slight differences between initial entries and
introduce a bias on the predictions. When a mutation is mod-
eled on top of an output A3D structure, the structures will
have the same starting background.- After download, .pdb files can be opened with specific any
software for 3D protein visualization, although we recommend
the use of PyMOL. - Despite the sequential plot and the score-table to gather a
general idea of the protein aggregation propensity landscape,
it has to be taken into account that propensities are not esti-
mated based on the primary sequence. Moreover, for globular
proteins most of the A3D detected APRs are built from amino
acids occurring in sequentially distant regions of the protein.
For this reason, A3D plots usually show profiles in which
several aggregation prone regions seem to be isolated on the
sequence, whereas in reality they are constituents of structural
APRs (Fig.3a). - RMSD values of the dynamic output should be taken with
caution since they only account for one of the multiple struc-
tures generated during backbone simulations. As a conse-
quence, the relative distances displayed in the interface are
not the average values for the protein, but serve as a frozen-
picture of the most aggregation-prone conformation.
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