the main players involved in virus entry. Variants of the protein
found in various species show different propensity to be targeted by
the virus. Suzuki used this fact in his computational study. He
prepared models of various variants of SLAM and performed dock-
ing of the viral protein with ClusPro. It turned out that the docking
score values appropriately ranked SLAM variants with different
potential of viral protein binding. Suzuki proposes this approach
as a possible method for evaluation of the risk of viral interspecies
transmission.
Another valuable application of PPD to understand viral infec-
tion mechanisms was reported by Dar et al. [43]. They focused on
the problem of the Zika virus infections. The problem is important,
since there is an increase in the number of infections, while there is
no FDA approved drug for Zika treatment. Dar et al. investigated
interactions of Zika non-structural protein 5 (NS5) with targets in
human cells, i.e., signal transducer and activator of transcription
2 (STAT2) and seven in absenthia homolog 2 (SIAH2). The study
contributes to understanding of how the virus decreases antiviral
response in infected individuals. The input was carefully elaborated;
for example, the authors prepared the input structures with short
molecular dynamics simulations instead of utilizing rough mini-
mized X-ray structures. The docking step was performed with
HADDOCK.
While studies of Dar et al. and of Suzuki touch the problem of
viral infections, a recent work of Antal et al. utilizes viral proteins for
a more general study [44]. They use a viral capsid protein as an
example of a protein with multiple interaction surfaces, capable of
spontaneous hierarchical oligomerization into capsids. For
instance, they use Rosetta and Amber for rescoring the results.
Rosetta and ZDOCK were used for blind docking. Their approach
allowed for estimation of possible oligomerization order, starting
from dimer formation and further to higher-order complexes.
Mechanisms of bacterial infections can also be elucidated with
PPD. Such efforts can support design of efficient vaccines. For
instance, Hossain et al. recently examined antigenic proteins of
Mycobacterium tuberculosis[45]. The aim of their study was to
find a bacterial protein suitable as a target for potential vaccines.
The initial search performed with Vaxign server [46] suggested that
the extracellular protein 85B might be a favorable target. Subse-
quently, the docking simulation with Molsoft ICM pro [47] was
used to investigate interactions of the epitope with the major
histocompatibility complex proteins (MHC).
MHC is a group of protein complexes responsible for proces-
sing of antigens and presenting them to T lymphocytes. Rawal et al.
recently investigated an MHC complex called DM, formed by
association of DMa and DMb subunits [48]. They used the Com-
puted Atlas of Surface Topography of Protein (CASTp) server [49]
to find putative residues participating in the interaction. The292 Agnieszka A. Kaczor et al.