Docking of protein models

An adequate description of entire genomes has to include information on the three‐dimensional (3D) structure of proteins. Most of these protein structures will be determined by high‐throughput modeling procedures. Thus, a structure‐based analysis of the network of protein–protein interactions in genomes requires docking methodologies that are capable of dealing with significant structural inaccuracies in the modeled structures of proteins. We present a systematic study of the applicability of our low‐resolution docking method to protein models of different accuracies. A representative nonredundant set of 475 cocrystallized protein–protein complexes was used to build an array of models of each protein in the set. A sophisticated procedure was created to generate the models with RMS deviations of 1, 2, 3, …, 10 Å from the crystal structure. The docking was performed for all the models, and the predictions were compared with the configurations of the original cocrystallized complexes. Statistical analysis showed that the low‐resolution docking can determine the gross structural features of protein–protein interactions for a significant percent of complexes of highly inaccurate protein models. Such predictions may serve as starting points for a more detailed structural analysis, as well as complement experimental and computational data on protein–protein interactions obtained by other techniques.