Estimation and filtering of potential protein-protein docking positions

Motivation: Software systems predicting automatically whether and how two proteins may interact are highly desirable, both for under-standing biological processes and for the rational design of new proteins. As a part of a future complete solution to this problem, a bundle of programs is presented designed (i) to estimate initial docking positions for a given pail of docking candidates, (ii) to adjust them, and (iii) to filter, them, thus preparing mole detailed computations of free energies. Results: The system is evaluated on a test set of 51 co-crystallized 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 rest set. The number of solutions is fixed to 50 positions with a median CPU time of 26 min. For 30 complexes, these contain a near-correct Solution with root mean square deviation (RMSD) less than or equal to 5.0 Angstrom, which is ranked first in five cases. For all complexes, the best solution is scored on rank 16 as the wet-st case, and has a median RMSD of 4.3 Angstrom.. Alter-natively to this initial estimation of docking positions, a global sampling of rotations was tested. Whereas this yields top-ranked solutions with RMSD less than or equal to 3.0 Angstrom for all 51 complexes, the median CPU time increases to 11 h. This shows that this blind sampling is not feasible for most applications.