Estimation and ltering of potential protein { protein docking positionsFriedrich

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 lter 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 sub-units. 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 xed to 50 positions with a median CPU{time of 26min. For 30 complexes these contain a near{correct solution