Structural characterization of protein-protein interactions is essential for understanding life processes. However, only a fraction of known proteins and, especially their complexes, have experimentally determined structures. Such structures can serve as templates for modeling protein interactions, where, in turn, individual proteins themselves will be model structures. However, development of reliable docking techniques for such task is largely hindered by the absence of carefully curated benchmark sets of template and model structures. We present two such sets, one consisting of 4950 full and 5936 interface-only structures (template sets) and another, containing 6 model structures with the distortion levels from 1 to 6 Å for 165 X-ray structures (model set). High structural quality of the template sets was achieved by automated procedures and manual curation. Redundancy in the template sets was removed by clustering the PDB structures based on structural similarity. The value of the clustering threshold was determined from the analysis of the clusters and the docking performance. The structures in the model set were generated by an approach mimicking actual protein modelling. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be achieved using these model structures. Both sets are integrated in the DOCKGROUND on-line system for docking studies (http://dockground.bioinformatics.ku.edu).

Template and model sets of protein structures

249th National Meeting (2015)

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