The capacity A3D to quickly generate mutated versions of a
given structure with the mutation tool is according to our records
the most used feature of this algorithm. As commented before,
genetically encoded amino acidic changes are linked to the out-
break of several conformational diseases and associated with the
severity of their symptoms [1]. Hence, A3D represents a useful tool
to model aggressive protein mutations to further redesign them, in
order to extend our knowledge about their implications in disease,
and, eventually, generate lead therapeutic compounds using this
structural knowledge. In the same way, A3D mutation modeling
can be used to enhance the solubility of proteins with biotechno-
logical interest, such as antibodies [45], or any protein with bio-
logic or biomedical relevance [46, 47]. A3D can be also used for
the screening and evaluation of large mutational protein data sets
[33] or as an alternative to phage display-like experimental
approaches.Fig. 4A3D performance. (a,b) A3D static run at 10 A ̊of the oligomerization domain of p53 corresponding to
the 3SAK pdb code. Monomeric chain (a) and tetrameric structure (b). Residues are colored following the A3D
scale in which blue means solubility and red aggregation. (c) and (d) runs at 10 A ̊of the DNA-binding domain
of p53 corresponding to the 2FEJ pdb code. Static mode (c) and dynamic mode (d). Residues are colored as in
(a) and (b)
438 Jordi Pujols et al.