  We explored the Protein DataBank (PDB) to collect protein-ssDNA structures
and create a multiconformational docking benchmark including both bound and
unbound protein structures. Due to ssDNA high flexibility when not bound, no
ssDNA unbound structure is included in the benchmark. For the 91
sequence-identity groups identified as bound-unbound structures of the same
protein, we studied the conformational changes in the protein induced by the
ssDNA binding. Moreover, based on several bound or unbound protein structures
in some groups, we also assessed the intrinsic conformational variability in
either bound or unbound conditions, and compared it to the supposedly
binding-induced modifications. To illustrate a use case of this benchmark, we
performed docking experiments using ATTRACT docking software. This benchmark
is, to our knowledge, the first one made to peruse available structures of
ssDNA-protein interactions to such an extent, aiming to improve computational
docking tools dedicated to this kind of molecular interactions.
