| Abstract | Motivation: Software systems predicting automatically whether and
how two proteins may interact are highly desirable, both, for understanding
biological processes and for rational design of new proteins. As
a part of a future complete solution to this problem a bundle of
programs is presented designed (1) to estimate initial docking positions
for a given pair of docking candidates, (2) to adjust them, and (3)
to filter them, thus preparing more detailed computations of free
energies. Results: The system is evaluated on a test set of 51 cocrystallized
complexes aiming at redocking the subunits. It works completely automatically
and the evaluation is performed using one single set of parameters
for all complexes in the test set. The number of solutions is fixed
to 50 positions with a median CPU-time of 26min. For 30 complexes
these contain a near-correct solution with RMSD <= 5.0 Angstrom,
which is ranked first in five cases. For all complexes the best solution
is scored on rank 16 as the worst case, and has a median RMSD of
4.3 Angstrom. Alternatively to this initial estimation of docking
positions a global sampling of rotations was tested. Whereas this
yields top-ranked solutions with RMSD <= 3.0 Angstrom for all
51 complexes the median CPU-time increases to 11h. This shows, that
this blind sampling is not feasible for most applications. Availability:
The system and its components are available on request from the authors.
Contact: E-mail addresses: friedric@techfak.uni-bielefeld or posch@techfak.uni-bielefeld.de. |
