Docking with Application in Cn Symmetric Multim"
February 3, 2006
Computational protein docking
is a useful technique for gaining insights into
protein interactions. We have developed an algorithm
M-ZDOCK for predicting the structure of cyclically
symmetric (Cn) multimers based on the structure
of an unbound (or partially bound) monomer.
Using a grid-based Fast Fourier Transform approach,
a space of exclusively symmetric multimers is
searched for the best structure. This leads
to improvements both in accuracy and running
time over the alternative, which is to run a
binary docking program ZDOCK and filter the
results for near-symmetry. The accuracy is improved
because fewer false positives are considered
in the search, thus hits are not as easily overlooked.
By searching four instead of six degrees of
freedom, the required amount of computation
is reduced. This program has been tested on
several known multimer complexes from the Protein
DataBank, including four unbound multimers:
three trimers and a pentamer. For all of these
cases, M-ZDOCK was able to find at least one
hit, whereas only two of the four test cases
had hits when using ZDOCK and a symmetry filter.
In addition, the running times are 30-40% faster