Estimation and filtering of potential protein-protein docking positions

Bioinformatics
F AckermannG Sagerer

Abstract

Software systems predicting automatically whether and how two proteins may interact are highly desirable, both for understanding 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 pair of docking candidates, (ii) to adjust them, and (iii) to filter them, thus preparing more detailed computations of free energies. 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 test 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 ) </=5.0 A, 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 A. 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 A for all 51 complexes,...Continue Reading

Citations

Jun 5, 2010·Journal of Molecular Modeling·Pralay Mitra, Debnath Pal
Jul 18, 2006·BMC Bioinformatics·Philipp Heuser, Dietmar Schomburg
Mar 11, 2008·Biophysical Chemistry·Shan ChangCun-xin Wang
May 27, 2004·Proteins·Alexander BerchanskiMiriam Eisenstein
Jul 17, 2004·Comptes rendus biologies·Miriam Eisenstein, Ephraim Katchalski-Katzir
Mar 1, 2000·Methods : a Companion to Methods in Enzymology·C A SotrifferJ M Varga

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