3.2 Run Options In the lower panel of the submission box named ‘options’the user
can name the project and introduce an e-mail address in order to be
notified immediately after A3D ends the prediction (seeNote 6). If
needed, due to confidentiality issues, it is possible to hide a project
from the queue list by ticking the option “do not show my job on the
results page”(seeNote 7). There are different possibilities to run
A3D and the user should use those that are more appropriate for
the protein under investigation.
l Static/dynamic: By default, A3D operates in static mode,
which is more tolerant in terms of input properties. In addition,
the absence of simulations provides the static mode with a
remarkable speed as compared to the dynamic version of A3D
(approximately 15 min vs 2 h for each run). However, in certain
occasions, the prediction of structural APRs requires dynamic
simulations in order to be biologically/biotechnologically rele-
vant (seeNote 8). Chose “Yes”onDynamic Mode in those
situations.
l Mutate: A3D integrates a useful tool which can be exploited to
virtually mutate any amino acid of the protein structure into a
different natural residue, select “Yes”onmutate residues. After
Fig. 2Front page. Schematic view of the different options the user can select for an A3D calculation
432 Jordi Pujols et al.