Modeling and minimizing CAPRI round 30 symmetrical protein complexes from CASP‐11 structural models

ABSTRACT Many of the modeling targets in the blind CASP‐11/CAPRI‐30 experiment were protein homo‐dimers and homo‐tetramers. Here, we perform a retrospective docking‐based analysis of the perfectly symmetrical CAPRI Round 30 targets whose crystal structures have been published. Starting from the CASP “stage‐2” fold prediction models, we show that using our recently developed “SAM” polar Fourier symmetry docking algorithm combined with NAMD energy minimization often gives acceptable or better 3D models of the target complexes. We also use SAM to analyze the overall quality of all CASP structural models for the selected targets from a docking‐based perspective. We demonstrate that docking only CASP “center” structures for the selected targets provides a fruitful and economical docking strategy. Furthermore, our results show that many of the CASP models are dockable in the sense that they can lead to acceptable or better models of symmetrical complexes. Even though SAM is very fast, using docking and NAMD energy minimization to pull out acceptable docking models from a large ensemble of docked CASP models is computationally expensive. Nonetheless, thanks to our SAM docking algorithm, we expect that applying our docking protocol on a modern computer cluster will give us the ability to routinely model 3D structures of symmetrical protein complexes from CASP‐quality models. Proteins 2017; 85:463–469. © 2016 Wiley Periodicals, Inc.